4D5Y | pdb_00004d5y

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	MNNL	e4d5yI1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
H	MNNL	e4d5yH1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
G	MNNL	e4d5yG1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
F	MNNL	e4d5yF1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
E	Ribosomal_S9	e4d5yE1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_S9	ECOD (v294.2)
QA [auth u]	MNNL	e4d5yu1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
PA [auth t]	Mtrc-MtrF_II-IV_dom	e4d5yt1	A: beta barrels	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: Mtrc-MtrF_II-IV_dom	ECOD (v294.2)
OA [auth p]	MNNL	e4d5yp1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
NA [auth o]	MNNL	e4d5yo1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
D	MNNL	e4d5yD1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
MA [auth n]	MNNL	e4d5yn1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
LA [auth m]	Ig_3	e4d5ym1	A: beta barrels	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: Ig_3	ECOD (v294.2)
KA [auth l]	MNNL	e4d5yl1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
JA [auth k]	V_ATPase_I	e4d5yk1	A: beta barrels	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.2)
IA [auth j]	MNNL	e4d5yj1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
HA [auth i]	Ig_3	e4d5yi1	A: beta barrels	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: Ig_3	ECOD (v294.2)
GA [auth h]	N6_Mtase	e4d5yh1	A: beta barrels	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.2)
FA [auth g]	V_ATPase_I	e4d5yg1	A: beta barrels	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.2)
EA [auth f]	MNNL	e4d5yf1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
DA [auth e]	MNNL	e4d5ye1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
C	Phosphodiest, Metalloenzyme	e4d5yC1	A: beta barrels	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.2)
CA [auth d]	MNNL	e4d5yd1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
BA [auth c]	MNNL	e4d5yc1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
AA [auth b]	V_ATPase_I	e4d5yb1	A: beta barrels	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.2)
Z [auth a]	Tudor_2	e4d5ya1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: Tudor_2	ECOD (v294.2)
Y [auth Z]	IQ,Myosin_tail_1	e4d5yZ1	A: beta barrels	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: IQ,Myosin_tail_1	ECOD (v294.2)
X [auth Y]	MNNL	e4d5yY1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
W [auth X]	N6_Mtase	e4d5yX1	A: beta barrels	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.2)
V [auth W]	MNNL	e4d5yW1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
U [auth V]	MNNL	e4d5yV1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
T [auth U]	MNNL	e4d5yU1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
B	MNNL	e4d5yB1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
S [auth T]	N6_Mtase	e4d5yT1	A: beta barrels	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.2)
R [auth S]	N6_Mtase	e4d5yS1	A: beta barrels	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.2)
Q [auth R]	MNNL	e4d5yR1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
P [auth Q]	MNNL	e4d5yQ1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
O [auth P]	MNNL	e4d5yP1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
N [auth O]	MNNL	e4d5yO1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
M [auth N]	MNNL	e4d5yN1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
L [auth M]	MNNL	e4d5yM1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
K [auth L]	V_ATPase_I	e4d5yL1	A: beta barrels	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: V_ATPase_I	ECOD (v294.2)
J	MNNL	e4d5yJ1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)
A	MNNL	e4d5yA1	A: beta barrels	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: MNNL	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03947	Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)	Ribosomal Proteins L2, C-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I	60S RIBOSOMAL PROTEIN UL16	-	-	-
H	60S RIBOSOMAL PROTEIN UL6	-	-	-
G	60S RIBOSOMAL PROTEIN EL8	-	-	-
F	60S RIBOSOMAL PROTEIN UL30	-	-	-
E	60S RIBOSOMAL PROTEIN EL6	-	-	-
TA [auth 4]	5S Ribosomal RNA	-	-	-
SA [auth 3]	5.8S Ribosomal RNA	-	-	-
RA [auth 2]	28S Ribosomal RNA	-	-	-
QA [auth u]	60S RIBOSOMAL PROTEIN UL1	-	-	-
PA [auth t]	60S RIBOSOMAL PROTEIN EL28	-	-	-
OA [auth p]	60S RIBOSOMAL PROTEIN EL43	-	-	-
NA [auth o]	60S RIBOSOMAL PROTEIN EL44	-	-	-
D	60S RIBOSOMAL PROTEIN UL18	-	-	-
MA [auth n]	60S RIBOSOMAL PROTEIN EL41	-	-	-
LA [auth m]	60S RIBOSOMAL PROTEIN EL40	-	-	-
KA [auth l]	60S RIBOSOMAL PROTEIN EL39	-	-	-
JA [auth k]	60S RIBOSOMAL PROTEIN EL38	-	-	-
IA [auth j]	60S RIBOSOMAL PROTEIN EL37	-	-	-
HA [auth i]	60S RIBOSOMAL PROTEIN EL36	-	-	-
GA [auth h]	60S RIBOSOMAL PROTEIN UL29	-	-	-
FA [auth g]	60S RIBOSOMAL PROTEIN EL34	-	-	-
EA [auth f]	60S RIBOSOMAL PROTEIN EL33	-	-	-
DA [auth e]	60S RIBOSOMAL PROTEIN EL32	-	-	-
C	60S RIBOSOMAL PROTEIN UL4	-	-	-
CA [auth d]	60S RIBOSOMAL PROTEIN EL31	-	-	-
BA [auth c]	60S RIBOSOMAL PROTEIN EL30	-	-	-
AA [auth b]	60S RIBOSOMAL PROTEIN EL29	-	-	-
Z [auth a]	60S RIBOSOMAL PROTEIN UL15	-	-	-
Y [auth Z]	60S RIBOSOMAL PROTEIN EL27	-	-	-
X [auth Y]	60S RIBOSOMAL PROTEIN UL24	-	-	-
W [auth X]	60S RIBOSOMAL PROTEIN UL23	-	-	-
V [auth W]	60S RIBOSOMAL PROTEIN EL24	-	-	-
U [auth V]	60S RIBOSOMAL PROTEIN UL14	-	-	-
T [auth U]	60S RIBOSOMAL PROTEIN EL22	-	-	-
B	60S RIBOSOMAL PROTEIN UL3	-	-	-
S [auth T]	60S RIBOSOMAL PROTEIN EL21	-	-	-
R [auth S]	60S RIBOSOMAL PROTEIN EL20	-	-	-
Q [auth R]	60S RIBOSOMAL PROTEIN UL19	-	-	-
P [auth Q]	60S RIBOSOMAL PROTEIN EL18	-	-	-
O [auth P]	60S RIBOSOMAL PROTEIN UL22	-	-	-
N [auth O]	60S RIBOSOMAL PROTEIN UL13	-	-	-
M [auth N]	60S RIBOSOMAL PROTEIN EL15	-	-	-
L [auth M]	60S RIBOSOMAL PROTEIN EL14	-	-	-
K [auth L]	60S RIBOSOMAL PROTEIN EL13	-	-	-
J	60S RIBOSOMAL PROTEIN UL5	-	-	-
A	60S RIBOSOMAL PROTEIN UL2	RNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023672	Large ribosomal subunit protein uL2, archaea/eukaryota	Family
A	IPR022669	Large ribosomal subunit protein uL2, C-terminal	Domain
A	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
A	IPR022671	Large ribosomal subunit protein uL2, conserved site	Conserved Site
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR022666	Large ribosomal subunit protein uL2, RNA-binding domain	Domain
A	IPR014726	Large ribosomal subunit protein uL2, domain 3	Homologous Superfamily
A	IPR002171	Large ribosomal subunit protein uL2	Family

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.