7PEL | pdb_00007pel

CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth F]	SCOP2B Superfamily	ARM repeat-like	8043105	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8043105	3000116	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)
H [auth F]	B56	e7pelF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: B56	ECOD (1.6)
C	B56	e7pelC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: B56	ECOD (1.6)
B	IN_DBD_C	e7pelB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
B	F_UNCLASSIFIED	e7pelB3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)
B	rve	e7pelB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
G [auth E]	IN_DBD_C	e7pelE2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
G [auth E]	F_UNCLASSIFIED	e7pelE3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth E]	rve	e7pelE1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
F [auth D]	IN_DBD_C	e7pelD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
F [auth D]	F_UNCLASSIFIED	e7pelD2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth D]	rve	e7pelD3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
A	IN_DBD_C	e7pelA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
A	F_UNCLASSIFIED	e7pelA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)
A	rve	e7pelA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
G [auth E]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
F [auth D]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, H [auth F]	PF01603	Protein phosphatase 2A regulatory B subunit (B56 family) (B56)	Protein phosphatase 2A regulatory B subunit (B56 family)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth L], J [auth N]	DNA (5'-D(GPAPGPAPGPAPAPGPCPGPCPCPAPAPAPCPAPCP*A)-3')	-	-	-
D [auth K], I [auth M]	DNA (5'-D(APCPTPGPTPGPTPTPTPGPGPCPGPCPTPTPCPTPCPTP*C)-3')	-	-	-
C, H [auth F]	Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform	DNA binding double-stranded DNA binding binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding double-stranded DNA binding binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA processing ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA processing cellular component organization or biogenesis mRNA splice site recognition RNA splicing protein-containing complex organization primary metabolic process mRNA 5'-splice site recognition gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process response to oxidative stress response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process chromatin organization chromatin remodeling organelle organization chromosome organization sister chromatid cohesion cell cycle meiotic sister chromatid cohesion cell cycle process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process cellular response to stimulus signaling signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication cellular response to stress DNA damage response signal transduction in response to DNA damage signal transduction cell death intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage apoptotic process intrinsic apoptotic signaling pathway programmed cell death 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 ubiquitin-dependent protein catabolic process protein metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen euchromatin nucleoplasm phosphatase complex protein-containing complex catalytic complex protein phosphatase type 2A complex protein serine/threonine phosphatase complex Golgi apparatus endomembrane system chromosome, centromeric region chromosomal region
A, B, F [auth D], G [auth E]	Pol protein	DNA binding binding nucleic acid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity DNA binding binding nucleic acid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding RNA stem-loop binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process viral genome integration into host DNA DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, H [auth F]	IPR021567	Lens epithelium-derived growth factor, integrase-binding domain	Domain
C, H [auth F]	IPR036218	HIV integrase-binding domain superfamily	Homologous Superfamily
C, H [auth F]	IPR000313	PWWP domain	Domain
C, H [auth F]	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily
C, H [auth F]	IPR016024	Armadillo-type fold	Homologous Superfamily
C, H [auth F]	IPR002554	Protein phosphatase 2A, regulatory B subunit, B56	Family
C, H [auth F]	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B, F [auth D], G [auth E]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, F [auth D], G [auth E]	IPR002156	Ribonuclease H domain	Domain
A, B, F [auth D], G [auth E]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, F [auth D], G [auth E]	IPR001584	Integrase, catalytic core	Domain
A, B, F [auth D], G [auth E]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, F [auth D], G [auth E]	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, F [auth D], G [auth E]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, F [auth D], G [auth E]	IPR000477	Reverse transcriptase domain	Domain
A, B, F [auth D], G [auth E]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, H [auth F]	Pharos: Q13362	acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma progressive supranuclear palsy tuberculosis dermatomyositis hepatocellular carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma B-cell chronic lymphocytic leukemia Chromosomal Instability astrocytic tumor dermatomyositis gastric carcinoma lymphoplasmacytic lymphoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease thyroid gland papillary carcinoma interstitial cystitis malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis tuberculosis familial nonmedullary thyroid carcinoma large cell medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.