1CVJ | pdb_00001cvj

X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN COMPLEX WITH POLYADENYLATE RNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P [auth H]	d1cvjh1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O [auth G]	d1cvjg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N [auth F]	d1cvjf1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M [auth E]	d1cvje1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L [auth D]	d1cvjd1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K [auth C]	d1cvjc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth B]	d1cvjb1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I [auth A]	d1cvja1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Poly(A)-binding protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P [auth H]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
O [auth G]	SCOP2B Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2B (2022-06-29)
O [auth G]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
N [auth F]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
M [auth E]	SCOP2B Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2B (2022-06-29)
M [auth E]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
L [auth D]	SCOP2B Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2B (2022-06-29)
J [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2B (2022-06-29)
I [auth A]	SCOP2 Family	Canonical RBD	8022968	4000236	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Family	Canonical RBD	8022969	4000236	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	RNA-binding domain, RBD	8035348	3000110	SCOP2 (2022-06-29)
I [auth A]	SCOP2 Superfamily	RNA-binding domain, RBD	8035349	3000110	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P [auth H]	RRM_1	e1cvjH2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
P [auth H]	RRM_1_7	e1cvjH1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
O [auth G]	RRM_1	e1cvjG1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
O [auth G]	RRM_1_7	e1cvjG2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
N [auth F]	RRM_1	e1cvjF1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
N [auth F]	RRM_1_7	e1cvjF2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
M [auth E]	RRM_1	e1cvjE1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
M [auth E]	RRM_1_7	e1cvjE2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
L [auth D]	RRM_1	e1cvjD1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
L [auth D]	RRM_1_7	e1cvjD2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
K [auth C]	RRM_1	e1cvjC1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
K [auth C]	RRM_1_7	e1cvjC2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
J [auth B]	RRM_1	e1cvjB1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
J [auth B]	RRM_1_7	e1cvjB2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)
I [auth A]	RRM_1	e1cvjA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
I [auth A]	RRM_1_7	e1cvjA2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_7	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P [auth H]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
O [auth G]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
N [auth F]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
M [auth E]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
L [auth D]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
K [auth C]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
J [auth B]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
I [auth A]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	POLYADENYLATE BINDING PROTEIN 1	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding translation regulator activity translation activator activity poly(A) binding poly-purine tract binding single-stranded RNA binding poly-pyrimidine tract binding poly(U) RNA binding	regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process regulation of biological process regulation of cellular process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process nuclear-transcribed mRNA catabolic process negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological regulation negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biosynthetic process positive regulation of gene expression cellular process regulation of mRNA metabolic process post-transcriptional regulation of gene expression regulation of biological quality mRNA stabilization regulation of mRNA stability CRD-mediated mRNA stabilization RNA stabilization regulation of RNA stability positive regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay regulatory ncRNA-mediated gene silencing positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process positive regulation of cytoplasmic translation protein metabolic process regulation of protein metabolic process translation regulation of translation cytoplasmic translation regulation of cytoplasmic translation positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication RNA splicing nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule membrane membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle spliceosomal complex ribonucleoprotein complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol mCRD-mediated mRNA stability complex
A [auth M], B [auth N], C [auth O], D [auth P], E [auth Q], A [auth M], B [auth N], C [auth O], D [auth P], E [auth Q], F [auth R], G [auth S], H [auth T]	5'-R(APAPAPAPAPAPAPAPAPAP*A)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR002004	Polyadenylate-binding protein/Hyperplastic disc protein, C-terminal	Domain
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR006515	Polyadenylate binding protein, human types 1, 2, 3, 4	Family
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR003954	RNA recognition motif domain, eukaryotic-type	Domain
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR000504	RNA recognition motif domain	Domain
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR036053	PABC (PABP) domain	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR034364	PABP, RNA recognition motif 1	Domain
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	IPR045305	PABP, RNA recognition motif 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	Pharos: P11940	transitional cell carcinoma breast carcinoma urinary bladder cancer astrocytic tumor Down syndrome lung cancer Mammary Neoplasms, Human spina bifida urinary bladder neoplasm breast cancer Duchenne muscular dystrophy myopathy juvenile dermatomyositis ovarian cancer

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.