3J92 | pdb_00003j92

Structure and assembly pathway of the ribosome quality control complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	Ribosomal_L16	e3j92I1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Ribosomal protein L10e	F: Ribosomal_L16	ECOD (1.6)
H	Ribosomal_L6_2	e3j92H2	A: a+b two layers	X: Ribosomal protein L6 (From Topology)	H: Ribosomal protein L6 (From Topology)	T: Ribosomal protein L6	F: Ribosomal_L6_2	ECOD (1.6)
H	Ribosomal_L6	e3j92H1	A: a+b two layers	X: Ribosomal protein L6 (From Topology)	H: Ribosomal protein L6 (From Topology)	T: Ribosomal protein L6	F: Ribosomal_L6	ECOD (1.6)
G	Ribosomal_L7Ae_1	e3j92G1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
F	Ribosomal_L30_1	e3j92F1	A: a+b two layers	X: Ribosomal protein L30p/L7e (From Topology)	H: Ribosomal protein L30p/L7e (From Topology)	T: Ribosomal protein L30p/L7e	F: Ribosomal_L30_1	ECOD (1.6)
E	Ribosomal_L6e	e3j92E1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L6e	ECOD (1.6)
RA [auth u]	FbpA_1st	e3j92u1	A: beta barrels	X: MutM N-terminal domain-like	H: Fibrinogen binding protein N-terminal domain (From Topology)	T: Fibrinogen binding protein N-terminal domain	F: FbpA_1st	ECOD (1.6)
QA [auth t]	Ribosomal_L11	e3j92t1	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
QA [auth t]	Ribosomal_L11_N	e3j92t2	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)
PA [auth s]	Ribosomal_L10	e3j92s2	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein L10-like (From Topology)	T: Ribosomal protein L10-like	F: Ribosomal_L10	ECOD (1.6)
PA [auth s]	Ribosomal_P0_L10e	e3j92s1	A: a+b two layers	X: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)	H: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)	T: Insertion domain in 60S ribosomal protein rpP0 (L10P)	F: Ribosomal_P0_L10e	ECOD (1.6)
OA [auth r]	Ribosomal_L28e	e3j92r1	A: a+b two layers	X: RPL28 (From Topology)	H: RPL28 (From Topology)	T: RPL28	F: Ribosomal_L28e	ECOD (1.6)
NA [auth p]	Ribosomal_L37ae	e3j92p1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_L37ae	ECOD (1.6)
D	Ribosomal_L5e	e3j92D1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Ribosomal_L5e	ECOD (1.6)
MA [auth o]	Ribosomal_L44	e3j92o1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_L44	ECOD (1.6)
LA [auth m]	Ribosomal_L40e	e3j92m1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_L40e	ECOD (1.6)
KA [auth l]	Ribosomal_L39	e3j92l1	A: extended segments	X: Ribosomal protein L39e (From Topology)	H: Ribosomal protein L39e (From Topology)	T: Ribosomal protein L39e	F: Ribosomal_L39	ECOD (1.6)
JA [auth k]	Ribosomal_L38e	e3j92k1	A: a+b two layers	X: SRP9/14-like	H: Signal recognition particle alu RNA binding heterodimer SRP9/14-related (From Topology)	T: Signal recognition particle alu RNA binding heterodimer SRP9/14-related	F: Ribosomal_L38e	ECOD (1.6)
IA [auth j]	Ribosomal_L37e	e3j92j1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_L37e	ECOD (1.6)
HA [auth i]	Ribosomal_L36e	e3j92i1	A: alpha arrays	X: 60S ribosomal protein rpL36 (L36e) (From Topology)	H: 60S ribosomal protein rpL36 (L36e) (From Topology)	T: 60S ribosomal protein rpL36 (L36e)	F: Ribosomal_L36e	ECOD (1.6)
GA [auth h]	Ribosomal_L29_2	e3j92h1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p) (From Topology)	T: Ribosomal protein L29 (L29p)	F: Ribosomal_L29_2	ECOD (1.6)
FA [auth g]	Ribosomal_L34e	e3j92g1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: RPL34 (From Topology)	T: RPL34	F: Ribosomal_L34e	ECOD (1.6)
EA [auth f]	Ribosomal_L35Ae	e3j92f1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L35Ae	ECOD (1.6)
DA [auth e]	Ribosomal_L32e	e3j92e1	A: a/b three-layered sandwiches	X: Ribosomal protein L13/L15p/L18e/L32e	H: Ribosomal protein L32e (From Topology)	T: Ribosomal protein L32e	F: Ribosomal_L32e	ECOD (1.6)
C	Ribosomal_L4	e3j92C2	A: a/b three-layered sandwiches	X: Ribosomal protein L4 (From Topology)	H: Ribosomal protein L4 (From Topology)	T: Ribosomal protein L4	F: Ribosomal_L4	ECOD (1.6)
C	Ribos_L4_asso_C	e3j92C1	A: extended segments	X: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)	H: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)	T: C-terminal helical region in 60S ribosomal protein L4 (L4p)	F: Ribos_L4_asso_C	ECOD (1.6)
CA [auth d]	Ribosomal_L31e	e3j92d1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: Ribosomal_L31e	ECOD (1.6)
BA [auth c]	Ribosomal_L7Ae	e3j92c1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae	ECOD (1.6)
AA [auth b]	Ribosomal_L29e	e3j92b1	A: extended segments	X: RPL29 (From Topology)	H: RPL29 (From Topology)	T: RPL29	F: Ribosomal_L29e	ECOD (1.6)
Z [auth a]	Ribosomal_L18	e3j92a1	A: a/b three-layered sandwiches	X: Ribosomal protein L13/L15p/L18e/L32e	H: Ribosomal proteins L15p and L18e (From Topology)	T: Ribosomal proteins L15p and L18e	F: Ribosomal_L18	ECOD (1.6)
Y [auth Z]	Ribosomal_L27e	e3j92Z1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L27e	ECOD (1.6)
X [auth Y]	Ribosomal_L26	e3j92Y1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L26	ECOD (1.6)
W [auth X]	Ribosomal_L23_3	e3j92X1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal proteins S24e, L23 and L15e (From Topology)	T: Ribosomal proteins S24e, L23 and L15e	F: Ribosomal_L23_3	ECOD (1.6)
V [auth W]	Ribosomal_L24e	e3j92W1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: Ribosomal_L24e	ECOD (1.6)
U [auth V]	Ribosomal_L14	e3j92V1	A: beta barrels	X: Ribosomal protein L14-like	H: Ribosomal protein L14-related (From Topology)	T: Ribosomal protein L14-related	F: Ribosomal_L14	ECOD (1.6)
T [auth U]	Ribosomal_L22e	e3j92U1	A: a+b two layers	X: Ribosomal protein L22e (From Topology)	H: Ribosomal protein L22e (From Topology)	T: Ribosomal protein L22e	F: Ribosomal_L22e	ECOD (1.6)
B	Ribosomal_L3	e3j92B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L3	ECOD (1.6)
S [auth T]	Ribosomal_L21e	e3j92T1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L21e	ECOD (1.6)
R [auth S]	Ribosomal_L18A	e3j92S2	A: a+b two layers	X: GP2-like	H: RplX-like (From Topology)	T: RplX-like	F: Ribosomal_L18A	ECOD (1.6)
Q [auth R]	Ribosomal_L19e_N	e3j92R1	A: alpha arrays	X: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)	H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)	T: Ribosomal protein L19 (L19e) N-terminal domain	F: Ribosomal_L19e_N	ECOD (1.6)
Q [auth R]	Ribosomal_L19e_C	e3j92R2	A: alpha bundles	X: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)	H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)	T: Ribosomal protein L19 (L19e) C-terminal domain	F: Ribosomal_L19e_C	ECOD (1.6)
P [auth Q]	Ribosomal_L18	e3j92Q1	A: a/b three-layered sandwiches	X: Ribosomal protein L13/L15p/L18e/L32e	H: Ribosomal proteins L15p and L18e (From Topology)	T: Ribosomal proteins L15p and L18e	F: Ribosomal_L18	ECOD (1.6)
O [auth P]	Ribosomal_L22	e3j92P1	A: a+b two layers	X: Enolase-N/ribosomal protein	H: Ribosomal protein L22 (From Topology)	T: Ribosomal protein L22	F: Ribosomal_L22	ECOD (1.6)
N [auth O]	Ribosomal_L13	e3j92O1	A: a/b three-layered sandwiches	X: Ribosomal protein L13/L15p/L18e/L32e	H: Ribosomal protein L13 and L16-A (From Topology)	T: Ribosomal protein L13 and L16-A	F: Ribosomal_L13	ECOD (1.6)
M [auth N]	Ribosomal_L15e	e3j92N1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal proteins S24e, L23 and L15e (From Topology)	T: Ribosomal proteins S24e, L23 and L15e	F: Ribosomal_L15e	ECOD (1.6)
L [auth M]	Ribosomal_L14e	e3j92M1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L14e	ECOD (1.6)
K [auth L]	Ribosomal_L13e	e3j92L1	A: extended segments	X: RPL13 (From Topology)	H: RPL13 (From Topology)	T: RPL13	F: Ribosomal_L13e	ECOD (1.6)
J	Ribosomal_L5_C	e3j92J1	A: a+b two layers	X: Ribosomal protein L5 (From Topology)	H: Ribosomal protein L5 (From Topology)	T: Ribosomal protein L5	F: Ribosomal_L5_C	ECOD (1.6)
A	Ribosomal_L2_1	e3j92A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosomal_L2_1	ECOD (1.6)
A	Ribosomal_L2_C_2	e3j92A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L2_C_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
T [auth U]	PF05833	NFACT N-terminal and middle domains (NFACT_N)	NFACT N-terminal and middle domains	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I	uL16	-	-	-
H	uL6	-	-	-
G	eL8	-	-	-
F	eL30	-	-	-
CB [auth 8]	5.8S rRNA	-	-	-
BB [auth 7]	5S rRNA	-	-	-
E	eL6	-	-	-
AB [auth 5]	28S rRNA	-	-	-
ZA [auth 2]	tRNA	-	-	-
YA [auth 1]	nascent chain	-	-	-
UA [auth x], VA [auth y]	Listerin	-	-	-
TA [auth w], WA [auth z], XA [auth 0]	Listerin	ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity	cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process cellular component organization organelle organization organelle disassembly biosynthetic process translational elongation cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process protein metabolic process protein autoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process ribosome-associated ubiquitin-dependent protein catabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol protein-containing complex RQC complex
RA [auth u], SA [auth v]	NEMF	ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding RNA binding nucleic acid binding alpha-aminoacyl-tRNA binding tRNA binding	localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process nuclear export establishment of localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process nuclear export establishment of localization cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis cellular component disassembly ribosome disassembly rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process organelle organization organelle disassembly biosynthetic process translational elongation metabolic process macromolecule metabolic process protein metabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process ribosome-associated ubiquitin-dependent protein catabolic process CAT tailing cytoplasmic translation cytoplasmic translational elongation	intracellular organelle cellular anatomical structure intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol protein-containing complex RQC complex membrane-bounded organelle nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol protein-containing complex RQC complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
QA [auth t]	uL11	-	-	-
PA [auth s]	uL10	-	-	-
OA [auth r]	eL28	-	-	-
NA [auth p]	eL43	-	-	-
D	uL18	-	-	-
MA [auth o]	eL42	-	-	-
LA [auth m]	eL40	-	-	-
KA [auth l]	eL39	-	-	-
JA [auth k]	eL38	-	-	-
IA [auth j]	eL37	-	-	-
HA [auth i]	eL36	-	-	-
GA [auth h]	uL29	-	-	-
FA [auth g]	eL34	-	-	-
EA [auth f]	eL33	-	-	-
DA [auth e]	eL32	-	-	-
C	uL4	-	-	-
CA [auth d]	eL31	-	-	-
BA [auth c]	eL30	-	-	-
AA [auth b]	eL29	-	-	-
Z [auth a]	uL15	-	-	-
Y [auth Z]	eL27	-	-	-
X [auth Y]	uL24	-	-	-
W [auth X]	uL23	-	-	-
V [auth W]	eL24	-	-	-
U [auth V]	uL14	-	-	-
T [auth U]	eL22	-	-	-
B	uL3	-	-	-
S [auth T]	eL21	-	-	-
R [auth S]	eL20	-	-	-
Q [auth R]	eL19	-	-	-
P [auth Q]	eL18	-	-	-
O [auth P]	uL22	-	-	-
N [auth O]	uL13	-	-	-
M [auth N]	eL15	-	-	-
L [auth M]	eL14	-	-	-
K [auth L]	eL13	-	-	-
J	uL5	-	-	-
A	uL2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
TA [auth w], WA [auth z], XA [auth 0]	IPR016024	Armadillo-type fold	Homologous Superfamily
TA [auth w], WA [auth z], XA [auth 0]	IPR039795	E3 ubiquitin-protein ligase listerin	Family
TA [auth w], WA [auth z], XA [auth 0]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
TA [auth w], WA [auth z], XA [auth 0]	IPR011016	Zinc finger, RING-CH-type	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR056241	E3 ubiquitin-protein ligase listerin, HEAT-repeats region	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR011989	Armadillo-like helical	Homologous Superfamily
TA [auth w], WA [auth z], XA [auth 0]	IPR054476	E3 ubiquitin-protein ligase listerin, N-terminal domain	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR054477	E3 ubiquitin-protein ligase listerin, HEAT repeat region	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR054478	E3 ubiquitin-protein ligase listerin, ubiquitin conjugating domain	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR039804	Listerin, zinc finger, RING-type	Domain
TA [auth w], WA [auth z], XA [auth 0]	IPR001841	Zinc finger, RING-type	Domain
RA [auth u], SA [auth v]	IPR008532	NFACT, RNA-binding domain	Domain
RA [auth u], SA [auth v]	IPR021846	NFACT protein, C-terminal	Domain
RA [auth u], SA [auth v]	IPR051608	Ribosome Quality Control Complex Subunit NEMF	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
TA [auth w], WA [auth z], XA [auth 0]	Pharos: O94822	hereditary spastic paraplegia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia large cell medulloblastoma Pick disease ovarian cancer psoriasis
RA [auth u], SA [auth v]	Pharos: O60524	autism spectrum disorder glioblastoma malignant glioma ovarian cancer Pick disease Autism Spectrum Disorders hereditary spastic paraplegia medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy dermatomyositis lymphoplasmacytic lymphoma osteosarcoma peripheral neuropathy psoriasis