1ZC8

Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
J [auth K]	d1zc8k1	All beta proteins	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
K [auth Y]	d1zc8y1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor Tu (EF-Tu), domain 2	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
K [auth Y]	d1zc8y2	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	Elongation factor Tu (EF-Tu)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
K [auth Y]	d1zc8y3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor Tu (EF-Tu), N-terminal (G) domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth K]	SCOP2B Superfamily	Small protein B (SmpB)	8040098	3000956	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056513	3002024	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056510	3002022	SCOP2B (2022-06-29)
K [auth Y]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056511	3002024	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth K]	SmpB	e1zc8K1	A: beta barrels	X: OB-fold	H: Small protein B (SmpB) (From Topology)	T: Small protein B (SmpB)	F: SmpB	ECOD (1.6)
K [auth Y]	GTP_EFTU_D2_1	e1zc8Y1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
K [auth Y]	GTP_EFTU_D3	e1zc8Y2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
K [auth Y]	MnmE_helical_2nd	e1zc8Y3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J [auth K]	PF01668	SmpB protein (SmpB)	SmpB protein	-	Family
K [auth Y]	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
K [auth Y]	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
K [auth Y]	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	TLD 16S ribosomal RNA	-	-	-
J [auth K]	SsrA-binding protein	RNA binding binding organic cyclic compound binding nucleic acid binding	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process trans-translation translational elongation organic substance biosynthetic process metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process trans-translation translational elongation organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
K [auth Y]	Elongation factor Tu	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	-	intracellular anatomical structure cytoplasm cellular anatomical entity
B	H2 16S rRNA	-	-	-
C	H2b d mRNA	-	-	-
D [auth G]	protein kinase 4 mRNA	-	-	-
E [auth F]	H5 16S ribosomal RNA	-	-	-
F [auth H]	protein kinase 2 mRNA	-	-	-
G [auth I]	protein kinase 3	-	-	-
H [auth J]	protein kinase 4 mRNA	-	-	-
I [auth Z]	H44 16S ribosomal RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J [auth K]	IPR020081	SsrA-binding protein, conserved site	Conserved Site
J [auth K]	IPR023620	Small protein B	Homologous Superfamily
J [auth K]	IPR000037	SsrA-binding protein	Family
K [auth Y]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
K [auth Y]	IPR033720	Elongation factor Tu, domain 2	Domain
K [auth Y]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
K [auth Y]	IPR031157	Tr-type G domain, conserved site	Conserved Site
K [auth Y]	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
K [auth Y]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
K [auth Y]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
K [auth Y]	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
K [auth Y]	IPR005225	Small GTP-binding protein domain	Domain
K [auth Y]	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
K [auth Y]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.