6UHC

CryoEM structure of human Arp2/3 complex with bound NPFs

PDB DOI: https://doi.org/10.2210/pdb6UHC/pdb
EM Map EMD-20770: EMDB EMDataResource

Classification: CONTRACTILE PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017, Escherichia coli
Mutation(s): No

Deposited: 2019-09-27 Released: 2020-07-01
Deposition Author(s): Zimmet, A., van Eeuwen, T., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism.

Zimmet, A., Van Eeuwen, T., Boczkowska, M., Rebowski, G., Murakami, K., Dominguez, R.

(2020) Sci Adv 6: eaaz7651-eaaz7651

DOI: https://doi.org/10.1126/sciadv.aaz7651

Macromolecule Content

Total Structure Weight: 336.62 kDa
Atom Count: 14,680
Modelled Residue Count: 1,940
Deposited Residue Count: 3,008
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 3	A	418	Homo sapiens	Mutation(s): 0 Gene Names: ACTR3, ARP3
UniProt & NIH Common Fund Data Resources
Find proteins for P61158 (Homo sapiens) Explore P61158 Go to UniProtKB: P61158
PHAROS: P61158 GTEx: ENSG00000115091
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61158
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2	B	394	Homo sapiens	Mutation(s): 0 Gene Names: ACTR2, ARP2
UniProt & NIH Common Fund Data Resources
Find proteins for P61160 (Homo sapiens) Explore P61160 Go to UniProtKB: P61160
PHAROS: P61160 GTEx: ENSG00000138071
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61160
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 1B	C	372	Homo sapiens	Mutation(s): 0 Gene Names: ARPC1B, ARC41
UniProt & NIH Common Fund Data Resources
Find proteins for O15143 (Homo sapiens) Explore O15143 Go to UniProtKB: O15143
PHAROS: O15143 GTEx: ENSG00000130429
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15143
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 2	D	300	Homo sapiens	Mutation(s): 0 Gene Names: ARPC2, ARC34, PRO2446
UniProt & NIH Common Fund Data Resources
Find proteins for O15144 (Homo sapiens) Explore O15144 Go to UniProtKB: O15144
PHAROS: O15144 GTEx: ENSG00000163466
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15144
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 3	E	203	Homo sapiens	Mutation(s): 0 Gene Names: ARPC3, ARC21
UniProt & NIH Common Fund Data Resources
Find proteins for O15145 (Homo sapiens) Explore O15145 Go to UniProtKB: O15145
PHAROS: O15145 GTEx: ENSG00000111229
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15145
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 4	F	168	Homo sapiens	Mutation(s): 0 Gene Names: ARPC4, ARC20
UniProt & NIH Common Fund Data Resources
Find proteins for P59998 (Homo sapiens) Explore P59998 Go to UniProtKB: P59998
PHAROS: P59998 GTEx: ENSG00000241553
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59998
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 5	G	151	Homo sapiens	Mutation(s): 0 Gene Names: ARPC5, ARC16
UniProt & NIH Common Fund Data Resources
Find proteins for O15511 (Homo sapiens) Explore O15511 Go to UniProtKB: O15511
PHAROS: O15511 GTEx: ENSG00000162704
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15511
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural Wiskott-Aldrich syndrome protein	H, I	501	Mus musculus	Mutation(s): 0 Gene Names: Wasl
UniProt
Find proteins for Q91YD9 (Mus musculus) Explore Q91YD9 Go to UniProtKB: Q91YD9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91YD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B]	K [auth A], M [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Interactions & Density Focus chain K [auth A] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B]	J [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.9.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Zimmet, A.

van Eeuwen, T.

Dominguez, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM07391
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008275
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	F31-HL146077