6SWD | pdb_00006swd

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
I	SCOP2B Superfamily	Ribosomal protein S8	8094002	3000709	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	GS N-terminal domain-like	8093818	3000408	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	SIS domain/Ribosomal protein S2-like	8093792	3001397	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Ribosomal S3Ae-like	8094349	3002166	SCOP2B (2022-06-29)
S [auth 6]	SCOP2B Superfamily	Nucleic acid-binding proteins	8085842	3000135	SCOP2B (2022-06-29)
P [auth W]	SCOP2B Superfamily	Zn-binding ribosomal proteins	8095129	3001320	SCOP2B (2022-06-29)
O [auth V]	SCOP2B Superfamily	Ribosomal proteins S24e, L23 and L15e	8037389	3000210	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	Translational machinery components	8098828	3000571	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	50S Ribosomal protein L14-like	8093764	3000433	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)
I	Chlor_dismutase	e6swdI1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
H [auth G]	Chlor_dismutase	e6swdG1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
F [auth E]	Chlor_dismutase	e6swdE1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
E [auth D]	Chlor_dismutase	e6swdD1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
D [auth C]		e6swdC1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F:	ECOD (develop294)
C [auth B]	Chlor_dismutase	e6swdB1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
B [auth A]	Chlor_dismutase	e6swdA1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
S [auth 6]	Chlor_dismutase	e6swd61	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
Q [auth 0]	KWL1	e6swd01	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: KWL1	ECOD (develop294)
P [auth W]	Chlor_dismutase	e6swdW1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
O [auth V]	Chlor_dismutase	e6swdV1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
N [auth R]	Chlor_dismutase	e6swdR1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
M [auth Q]	Chlor_dismutase	e6swdQ1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
L [auth N]	Chlor_dismutase	e6swdN1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
K [auth M]	Chlor_dismutase	e6swdM1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)
J	Chlor_dismutase	e6swdJ1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.30.1370.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (utative)
I	3.30.1490.10	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
G [auth F]	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
C [auth B]	3.40.50.10490	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glucose-6-phosphate isomerase like protein	CATH (utative)
S [auth 6]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)
P [auth W]	2.20.25.100	Mainly Beta	Single Sheet	N-terminal domain of TfIIb	Ribosomal protein S27	CATH (utative)
O [auth V]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (utative)
M [auth Q]	1.10.287.10	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	S15/NS1, RNA-binding	CATH (utative)
K [auth M]	3.30.420.80	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I	30S ribosomal protein S8	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
H [auth G]	30S ribosomal protein S6e	structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
G [auth F]	30S ribosomal protein S5	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
F [auth E]	30S ribosomal protein S4e	RNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
E [auth D]	30S ribosomal protein S4	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
D [auth C]	Zn-ribbon RNA-binding protein involved in translation	-	-	-
C [auth B]	30S ribosomal protein S2	structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
B [auth A]	30S ribosomal protein S3Ae	structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
S [auth 6]	Translation initiation factor 1A	translation factor activity translation initiation factor activity RNA binding binding nucleic acid binding	-	-
R [auth 5]	mRNA	-	-	-
Q [auth 0]	30S ribosomal protein aL41	-	-	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
P [auth W]	30S ribosomal protein S27e	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
O [auth V]	30S ribosomal protein S24e	structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
N [auth R]	30S ribosomal protein S17	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
M [auth Q]	30S ribosomal protein S15	RNA binding small ribosomal subunit rRNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
L [auth N]	30S ribosomal protein S12	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
K [auth M]	30S ribosomal protein S11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
J	30S ribosomal protein S8e	structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
A [auth 2]	16S ribosomal RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I	IPR000630	Small ribosomal subunit protein uS8	Family
I	IPR047863	Small ribosomal subunit protein uS8, conserved site	Conserved Site
I	IPR035987	Small ribosomal subunit protein uS8 superfamily	Homologous Superfamily
H [auth G]	IPR001377	Small ribosomal subunit protein eS6	Family
H [auth G]	IPR018282	Small ribosomal subunit protein eS6, conserved site	Conserved Site
H [auth G]	IPR020924	Small ribosomal subunit protein eS6, archaea	Family
G [auth F]	IPR005711	Small ribosomal subunit protein uS5, eukaryota_archaea	Family
G [auth F]	IPR000851	Small ribosomal subunit protein uS5	Family
G [auth F]	IPR047866	Small ribosomal subunit protein uS5, archaea	Family
G [auth F]	IPR005324	Small ribosomal subunit protein uS5, C-terminal	Domain
G [auth F]	IPR013810	Small ribosomal subunit protein uS5, N-terminal	Domain
G [auth F]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
G [auth F]	IPR018192	Small ribosomal subunit protein uS5, N-terminal, conserved site	Conserved Site
G [auth F]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
F [auth E]	IPR018199	Small ribosomal subunit protein eS4, N-terminal, conserved site	Conserved Site
F [auth E]	IPR013843	Small ribosomal subunit protein eS4, N-terminal	Domain
F [auth E]	IPR002942	RNA-binding S4 domain	Domain
F [auth E]	IPR013845	Small ribosomal subunit protein eS4, central region	Domain
F [auth E]	IPR000876	Small ribosomal subunit protein eS4	Family
F [auth E]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
F [auth E]	IPR038237	Small ribosomal subunit protein eS4, central domain superfamily	Homologous Superfamily
F [auth E]	IPR041982	Small ribosomal subunit protein eS4, KOW domain	Domain
F [auth E]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
F [auth E]	IPR005824	KOW	Domain
E [auth D]	IPR018079	Small ribosomal subunit protein uS4, conserved site	Conserved Site
E [auth D]	IPR002942	RNA-binding S4 domain	Domain
E [auth D]	IPR001912	Small ribosomal subunit protein uS4, N-terminal	Domain
E [auth D]	IPR022802	Small ribosomal subunit protein uS4, archaea	Family
E [auth D]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
E [auth D]	IPR022801	Small ribosomal subunit protein uS4	Family
E [auth D]	IPR005710	Small ribosomal subunit protein uS4, eukaryota/archaea	Family
D [auth C]	IPR044720	Small ribosomal subunit protein aS21	Family
D [auth C]	IPR011668	Ribosomal protein aS21, zinc-binding pocket	Domain
C [auth B]	IPR023454	Small ribosomal subunit protein uS2, archaea	Family
C [auth B]	IPR023591	Small ribosomal subunit protein uS2, flavodoxin-like domain superfamily	Homologous Superfamily
C [auth B]	IPR018130	Small ribosomal subunit protein uS2, conserved site	Conserved Site
C [auth B]	IPR001865	Small ribosomal subunit protein uS2	Family
C [auth B]	IPR005707	Small ribosomal subunit protein uS2, eukaryota/archaea	Family
B [auth A]	IPR001593	Small ribosomal subunit protein eS1	Family
B [auth A]	IPR018281	Small ribosomal subunit protein eS1, conserved site	Conserved Site
B [auth A]	IPR030838	Small ribosomal subunit protein eS1, archaea	Family
S [auth 6]	IPR018104	Translation initiation factor 1A (eIF-1A), conserved site	Conserved Site
S [auth 6]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
S [auth 6]	IPR006196	RNA-binding domain, S1, IF1 type	Domain
S [auth 6]	IPR001253	Translation initiation factor 1A (eIF-1A)	Family
P [auth W]	IPR023407	Small ribosomal subunit protein eS27, zinc-binding domain superfamily	Homologous Superfamily
P [auth W]	IPR000592	Small ribosomal subunit protein eS27	Family
P [auth W]	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
O [auth V]	IPR001976	Small ribosomal subunit protein eS24	Family
O [auth V]	IPR012678	Ribosomal protein uL23/eL15/eS24 core domain superfamily	Homologous Superfamily
O [auth V]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
O [auth V]	IPR018098	Small ribosomal subunit protein eS24 conserved site	Conserved Site
N [auth R]	IPR019979	Small ribosomal subunit protein uS17, conserved site	Conserved Site
N [auth R]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
N [auth R]	IPR000266	Small ribosomal subunit protein uS17	Family
N [auth R]	IPR019978	Small ribosomal subunit protein uS17, archaeal	Family
N [auth R]	IPR028333	Small ribosomal subunit protein uS17, archaeal/eukaryotic	Family
M [auth Q]	IPR012606	Small ribosomal subunit protein uS15, N-terminal	Domain
M [auth Q]	IPR009068	uS15/NS1, RNA-binding domain superfamily	Homologous Superfamily
M [auth Q]	IPR023029	Small ribosomal subunit protein uS15, archaea/eukaryota	Family
M [auth Q]	IPR000589	Small ribosomal subunit protein uS15	Family
L [auth N]	IPR006032	Small ribosomal subunit protein uS12	Family
L [auth N]	IPR022863	Ribosomal protein uS12, archaea	Family
L [auth N]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
L [auth N]	IPR005680	Small ribosomal subunit protein uS12, eukaryota/archaea	Family
K [auth M]	IPR019961	Small ribosomal subunit protein uS11, archaea	Family
K [auth M]	IPR001971	Small ribosomal subunit protein uS11	Family
K [auth M]	IPR036967	Small ribosomal subunit protein uS11 superfamily	Homologous Superfamily
K [auth M]	IPR018102	Small ribosomal subunit protein uS11, conserved site	Conserved Site
J	IPR001047	Small ribosomal subunit protein eS8	Family
J	IPR020919	Small ribosomal subunit protein eS8, archaea	Family
J	IPR022309	Ribosomal protein eS8/ribosomal biogenesis NSA2	Family
J	IPR018283	Small ribosomal subunit protein eS8, conserved site	Conserved Site