4IMY | pdb_00004imy

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4imya_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4imyc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4imye_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4imyb1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	Cyclin T1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4imyd1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	Cyclin T1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4imyf1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	Cyclin T1	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)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039362	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039362	3000066	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039362	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8039367	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8039364	3000768	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8039364	3000768	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cyclin-like	8039367	3000768	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cyclin-like	8039364	3000768	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cyclin-like	8039367	3000768	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)
A	Pkinase	e4imyA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: Pkinase	ECOD (v294.1)
C	Pkinase	e4imyC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Pkinase	ECOD (v294.1)
E	ERG4_ERG24	e4imyE2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: N-terminal domain of Delta(14)-sterol reductase, MaSR1	F: ERG4_ERG24	ECOD (v294.1)
B	Ribosomal_S3_C	e4imyB5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Ribosomal_S3_C	ECOD (v294.1)
D	DIM1	e4imyD1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: DIM1	ECOD (v294.1)
F	Ribosomal_S3_C	e4imyF5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Ribosomal_S3_C	ECOD (v294.1)
G	Serpin	e4imyG01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Serpin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
E	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
E	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
D	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
F	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
H	6.10.250.2670	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
B, D, F	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
B, D, F	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Cyclin-dependent kinase 9	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding protein serine/threonine kinase activity histone H1-4S187 kinase activity catalytic activity, acting on a protein protein kinase activity phosphotransferase activity, alcohol group as acceptor histone H1 kinase activity histone modifying activity histone kinase activity RNA binding snRNA binding 7SK snRNA binding protein serine kinase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cyclin-dependent protein serine/threonine kinase activity cyclin-dependent protein kinase activity protein binding kinase binding enzyme binding protein kinase binding transcription factor binding transcription coregulator binding transcription coactivator binding transcription regulator activity transcription elongation factor activity RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process replication fork processing regulation of cellular process RNA metabolic process mRNA processing DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process replication fork processing regulation of cellular process RNA metabolic process mRNA processing regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing regulation of mRNA processing regulation of biological process mRNA 3'-end processing regulation of mRNA 3'-end processing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process biosynthetic process regulation of mRNA metabolic process regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II cell population proliferation developmental process regulation of developmental process cellular developmental process regulation of cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation anatomical structure development regulation of localization protein localization to chromatin regulation of protein localization negative regulation of biological process negative regulation of protein localization to chromatin localization protein localization to chromosome macromolecule localization protein localization to organelle intracellular protein localization regulation of protein localization to chromatin negative regulation of protein localization organelle localization nucleus localization DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair transcription elongation by RNA polymerase II transcription elongation-coupled chromatin remodeling cellular component organization DNA-templated transcription elongation chromatin organization chromatin remodeling cellular component organization or biogenesis host-mediated activation of viral transcription biological process involved in interspecies interaction between organisms host-mediated perturbation of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process positive regulation of biological process positive regulation of protein localization positive regulation of protein localization to chromatin positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule 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 DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II 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 cell cycle regulation of cell cycle regulation of cellular response to stress regulation of response to stress regulation of DNA repair regulation of response to stimulus regulation of DNA metabolic process response to peptide response to chemical response to cytokine cellular response to cytokine stimulus	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm catalytic complex cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups organelle lumen carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule P-TEFb complex nuclear body PML body
B, D, F	Cyclin-T1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase binding protein binding enzyme binding RNA binding snRNA binding 7SK snRNA binding cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity cyclin-dependent protein kinase regulator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity kinase binding protein kinase binding transcription factor binding DNA-binding transcription factor binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation 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 DNA-templated transcription elongation regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cell division transcription by RNA polymerase II host-mediated activation of viral transcription biological process involved in interspecies interaction between organisms host-mediated perturbation of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle cellular anatomical structure nucleoplasm catalytic complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle cellular anatomical structure nucleoplasm catalytic complex cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups organelle lumen carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen cytoplasm cytosol P-TEFb complex
G, H, I	AF4/FMR2 family member 4	-	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development germ cell development cellular response to stimulus cellular response to stress response to stimulus response to stress response to endoplasmic reticulum stress	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen fibrillar center organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen fibrillar center organelle membraneless organelle nuclear lumen euchromatin chromatin chromosome nuclear body nucleoplasm protein-containing complex transcription elongation factor complex nuclear protein-containing complex super elongation complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C, E	IPR000719	Protein kinase domain	Domain
A, C, E	IPR050108	Cyclin-dependent kinase	Family
A, C, E	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C, E	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D, F	IPR047320	Cyclin-T1, second cyclin box	Domain
B, D, F	IPR006671	Cyclin, N-terminal	Domain
B, D, F	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B, D, F	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B, D, F	IPR013763	Cyclin-like domain	Domain
G, H, I	IPR007797	AF4/FMR2 family	Family
G, H, I	IPR043640	AF4/FMR2, C-terminal homology domain	Domain
G, H, I	IPR043639	AF4 interaction motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E	Pharos: P50750	Gaucher disease
B, D, F	Pharos: O60563	acute myeloid leukemia osteosarcoma Pick disease juvenile dermatomyositis ovarian cancer psoriasis myopathy pancreatic ductal adenocarcinoma
G, H, I	Pharos: Q9UHB7	cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome obesity disorder Facies lung disease malignant glioma medulloblastoma non-small cell lung carcinoma osteosarcoma astrocytic tumor pancreatic intraductal papillary-mucinous carcinoma breast cancer large cell medulloblastoma malignant mesothelioma acquired metabolic disease ovarian cancer cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome obesity disorder Facies lung disease malignant glioma medulloblastoma non-small cell lung carcinoma osteosarcoma astrocytic tumor pancreatic intraductal papillary-mucinous carcinoma breast cancer large cell medulloblastoma malignant mesothelioma acquired metabolic disease ovarian cancer atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer genetic endocrine growth disease intellectual disability lung cancer malignant ependymoma malignant pancreatic neoplasm myopathy oligodendroglioma adenoma pancreatic ductal adenocarcinoma congenital heart disease glioblastoma juvenile dermatomyositis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.