3DWL

Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2 Family	WD40-repeat	8085896	4002744	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	WD40 repeat-like	8085897	3001694	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	WD40 repeat-like	8085897	3001694	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Arp2/3 complex subunits	8085061	3000751	SCOP2B (2022-06-29)
E [auth F]	SCOP2 Family	Arp2/3 complex subunits	8085060	4003389	SCOP2 (2022-06-29)
E [auth F]	SCOP2 Superfamily	Arp2/3 complex subunits	8085061	3000751	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00022	e3dwlA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
G [auth B]	PF00022	e3dwlB4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
B [auth C]	PF00400	e3dwlC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
H	PF00400	e3dwlH1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
I	PF04045	e3dwlI1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Arp2/3 complex subunits (From Topology)	T: Arp2/3 complex subunits	F: PF04045	ECOD (1.6)
C [auth D]	PF04045	e3dwlD1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Arp2/3 complex subunits (From Topology)	T: Arp2/3 complex subunits	F: PF04045	ECOD (1.6)
D [auth E]	PF04062	e3dwlE1	A: alpha bundles	X: Arp2/3 complex 21 kDa subunit ARPC3 (From Topology)	H: Arp2/3 complex 21 kDa subunit ARPC3 (From Topology)	T: Arp2/3 complex 21 kDa subunit ARPC3	F: PF04062	ECOD (1.6)
J	PF04062	e3dwlJ1	A: alpha bundles	X: Arp2/3 complex 21 kDa subunit ARPC3 (From Topology)	H: Arp2/3 complex 21 kDa subunit ARPC3 (From Topology)	T: Arp2/3 complex 21 kDa subunit ARPC3	F: PF04062	ECOD (1.6)
K	PF05856	e3dwlK1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Arp2/3 complex subunits (From Topology)	T: Arp2/3 complex subunits	F: PF05856	ECOD (1.6)
E [auth F]	PF05856	e3dwlF1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Arp2/3 complex subunits (From Topology)	T: Arp2/3 complex subunits	F: PF05856	ECOD (1.6)
F [auth G]	PF04699	e3dwlG1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Arp2/3 complex 16 KDa subunit ARPC5 (From Topology)	T: Arp2/3 complex 16 KDa subunit ARPC5	F: PF04699	ECOD (1.6)
L	PF04699	e3dwlL1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Arp2/3 complex 16 KDa subunit ARPC5 (From Topology)	T: Arp2/3 complex 16 KDa subunit ARPC5	F: PF04699	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
G [auth B]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G [auth B]	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
B [auth C]	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
H	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
I	3.30.1460.20	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
C [auth D]	3.30.1460.20	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
D [auth E]	6.10.20.160	Special	Helix non-globular	Arc Repressor Mutant, subunit A		CATH (4.3.0)
J	6.10.20.160	Special	Helix non-globular	Arc Repressor Mutant, subunit A		CATH (4.3.0)
K	3.30.1460.20	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
E [auth F]	3.30.1460.20	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
F [auth G]	1.25.40.190	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Actin-related protein 2/3 complex subunit 5	CATH (4.3.0)
L	1.25.40.190	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Actin-related protein 2/3 complex subunit 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, G [auth B]	PF00022	Actin (Actin)	Actin	-	Family
B [auth C], H	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
C [auth D], I	PF04045	Arp2/3 complex, 34 kD subunit p34-Arc (P34-Arc)	Arp2/3 complex, 34 kD subunit p34-Arc	-	Family
D [auth E], J	PF04062	ARP2/3 complex ARPC3 (21 kDa) subunit (P21-Arc)	ARP2/3 complex ARPC3 (21 kDa) subunit	-	Family
E [auth F], K	PF05856	ARP2/3 complex 20 kDa subunit (ARPC4) (ARPC4)	ARP2/3 complex 20 kDa subunit (ARPC4)	-	Family
F [auth G], L	PF04699	ARP2/3 complex 16 kDa subunit (p16-Arc) (P16-Arc)	ARP2/3 complex 16 kDa subunit (p16-Arc)	The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20 ...	The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, G [auth B]	Actin-related protein 3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding actin filament binding	actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process localization import into cell transport endocytosis establishment of localization vesicle-mediated transport protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization cellular component biogenesis cellular component assembly protein-containing complex assembly actin cortical patch organization cortical actin cytoskeleton organization cortical cytoskeleton organization	intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cytosol cell division site Arp2/3 protein complex protein-containing complex cell tip cell pole cell cortex region cell cortex of cell tip cytoplasmic region
B [auth C], H	Actin-related protein 2/3 complex subunit 1	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding	actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly cellular component biogenesis cellular component assembly cortical actin cytoskeleton organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport	cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cytosol cell division site Arp2/3 protein complex protein-containing complex
C [auth D], I	Actin-related protein 2/3 complex subunit 2	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding structural constituent of cytoskeleton structural molecule activity	actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly cellular component biogenesis cellular component assembly cortical actin cytoskeleton organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization protein-containing complex assembly	cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cytosol cell division site Arp2/3 protein complex protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D [auth E], J	Actin-related protein 2/3 complex subunit 3	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding	actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly cellular component biogenesis cellular component assembly cortical actin cytoskeleton organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport developmental process regulation of biological process regulation of developmental process establishment or maintenance of cell polarity regulating cell shape biological regulation regulation of cell shape establishment or maintenance of cell polarity cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis regulation of cytoskeleton organization regulation of cellular process regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly protein-containing complex assembly regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization regulation of actin polymerization or depolymerization regulation of cellular component biogenesis regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization regulation of anatomical structure size	cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton cell tip cell pole cellular anatomical entity intracellular anatomical structure cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cytosol cell division site Arp2/3 protein complex protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E [auth F], K	Actin-related protein 2/3 complex subunit 4	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding	protein polymerization actin polymerization or depolymerization actin filament polymerization actin cytoskeleton organization protein-containing complex organization actin filament organization cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly actin filament-based process cellular process cellular component organization or biogenesis protein polymerization actin polymerization or depolymerization actin filament polymerization actin cytoskeleton organization protein-containing complex organization actin filament organization cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization Arp2/3 complex-mediated actin nucleation actin nucleation actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly cortical actin cytoskeleton organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell cortex cortical cytoskeleton actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch non-membrane-bounded organelle Arp2/3 protein complex protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F [auth G], L	Actin-related protein 2/3 complex subunit 5	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding	actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly actin cytoskeleton organization actin filament organization Arp2/3 complex-mediated actin nucleation cellular component organization organelle organization actin filament-based process cellular process cellular component organization or biogenesis actin nucleation supramolecular fiber organization cytoskeleton organization actin cortical patch organization cortical cytoskeleton organization actin cortical patch assembly cellular component biogenesis cellular component assembly cortical actin cytoskeleton organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport regulation of cytoskeleton organization regulation of cellular process regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly protein-containing complex assembly regulation of actin filament polymerization regulation of biological quality protein polymerization actin polymerization or depolymerization regulation of biological process regulation of actin filament organization actin filament polymerization protein-containing complex organization biological regulation regulation of actin polymerization or depolymerization regulation of cellular component biogenesis regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization regulation of anatomical structure size	intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery endocytic patch cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton actin cortical patch cytoplasm non-membrane-bounded organelle cell projection mating projection cell tip mating projection tip cell pole plasma membrane bounded cell projection site of polarized growth cytosol Arp2/3 protein complex protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, G [auth B]	IPR020902	Actin/actin-like conserved site	Conserved Site
A, G [auth B]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, G [auth B]	IPR004000	Actin family	Family
B [auth C], H	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B [auth C], H	IPR017383	Actin-related protein 2/3 complex subunit 1	Family
B [auth C], H	IPR001680	WD40 repeat	Repeat
B [auth C], H	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth D], I	IPR034666	Arp2/3 complex subunit 2/4	Homologous Superfamily
C [auth D], I	IPR007188	Actin-related protein 2/3 complex subunit 2	Family
D [auth E], J	IPR007204	Actin-related protein 2/3 complex subunit 3	Family
D [auth E], J	IPR036753	Actin-related protein 2/3 complex subunit 3 superfamily	Homologous Superfamily
E [auth F], K	IPR034666	Arp2/3 complex subunit 2/4	Homologous Superfamily
E [auth F], K	IPR008384	Actin-related protein 2/3 complex subunit 4	Family
F [auth G], L	IPR006789	Actin-related protein 2/3 complex subunit 5	Family
F [auth G], L	IPR036743	Actin-related protein 2/3 complex subunit 5 superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.