Annotations: 6NIL

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	Core binding factor beta, CBF	8042548	3001169	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core binding factor beta, CBF	8042548	3001169	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core binding factor beta, CBF	8042548	3001169	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core binding factor beta, CBF	8042548	3001169	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	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)
L	Vif	e6nilL1	A: a+b two layers	X: Virion infectivity factor Vif (From Topology)	H: Virion infectivity factor Vif (From Topology)	T: Virion infectivity factor Vif	F: Vif	ECOD (1.6)
I	Vif	e6nilI1	A: a+b two layers	X: Virion infectivity factor Vif (From Topology)	H: Virion infectivity factor Vif (From Topology)	T: Virion infectivity factor Vif	F: Vif	ECOD (1.6)
F	Vif	e6nilF1	A: a+b two layers	X: Virion infectivity factor Vif (From Topology)	H: Virion infectivity factor Vif (From Topology)	T: Virion infectivity factor Vif	F: Vif	ECOD (1.6)
C	Vif	e6nilC1	A: a+b two layers	X: Virion infectivity factor Vif (From Topology)	H: Virion infectivity factor Vif (From Topology)	T: Virion infectivity factor Vif	F: Vif	ECOD (1.6)
K	CBF_beta	e6nilK1	A: beta barrels	X: CBF-like	H: Core binding factor beta, CBF (From Topology)	T: Core binding factor beta, CBF	F: CBF_beta	ECOD (1.6)
H	CBF_beta	e6nilH1	A: beta barrels	X: CBF-like	H: Core binding factor beta, CBF (From Topology)	T: Core binding factor beta, CBF	F: CBF_beta	ECOD (1.6)
E	CBF_beta	e6nilE1	A: beta barrels	X: CBF-like	H: Core binding factor beta, CBF (From Topology)	T: Core binding factor beta, CBF	F: CBF_beta	ECOD (1.6)
B	CBF_beta	e6nilB1	A: beta barrels	X: CBF-like	H: Core binding factor beta, CBF (From Topology)	T: Core binding factor beta, CBF	F: CBF_beta	ECOD (1.6)
J	APOBEC_N	e6nilJ1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
G	APOBEC_N	e6nilG1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
D	APOBEC_N	e6nilD1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
A	APOBEC_N	e6nilA1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	2.40.250.10	Mainly Beta	Beta Barrel	Polyomavirus Enhancer Binding Protein 2	Chain: A	CATH (utative)
H	2.40.250.10	Mainly Beta	Beta Barrel	Polyomavirus Enhancer Binding Protein 2	Chain: A	CATH (utative)
E	2.40.250.10	Mainly Beta	Beta Barrel	Polyomavirus Enhancer Binding Protein 2	Chain: A	CATH (utative)
B	2.40.250.10	Mainly Beta	Beta Barrel	Polyomavirus Enhancer Binding Protein 2	Chain: A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	PF00559	Retroviral Vif (Viral infectivity) protein (Vif)	Retroviral Vif (Viral infectivity) protein	-	Family
A, D, G, J	PF08210	APOBEC-like N-terminal domain (APOBEC_N)	APOBEC-like N-terminal domain	A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More sp ...	A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [1] (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates [2]. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	Virion infectivity factor	RNA binding binding nucleic acid binding	viral process viral life cycle	virion component cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region
B, E, H, K	Core-binding factor subunit beta	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity sequence-specific DNA binding DNA binding binding nucleic acid binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation immune system process anatomical structure development leukocyte differentiation RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process definitive hemopoiesis regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of leukocyte differentiation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation regulation of cell differentiation positive regulation of T cell differentiation positive regulation of CD8-positive, alpha-beta T cell activation regulation of cell development positive regulation of developmental process positive regulation of cell activation multicellular organism development T cell activation positive regulation of leukocyte activation alpha-beta T cell activation regulation of immune system process T cell differentiation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development positive regulation of alpha-beta T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of alpha-beta T cell differentiation regulation of developmental process CD8-positive, alpha-beta T cell differentiation positive regulation of biological process positive regulation of leukocyte cell-cell adhesion regulation of alpha-beta T cell differentiation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion alpha-beta T cell differentiation cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion regulation of cell adhesion positive regulation of CD8-positive, alpha-beta T cell differentiation regulation of T cell activation regulation of CD8-positive, alpha-beta T cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation regulation of CD8-positive, alpha-beta T cell activation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process myeloid cell differentiation anatomical structure maturation cell maturation developmental maturation negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation CD4-positive, alpha-beta T cell activation negative regulation of cell differentiation negative regulation of developmental process negative regulation of cell activation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of immune system process negative regulation of alpha-beta T cell activation	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, D, G, J	DNA dC->dU-editing enzyme APOBEC-3F	RNA binding binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding metal ion binding RNA binding binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cytidine to uridine editing RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification base conversion or substitution editing macromolecule modification negative regulation of viral process regulation of viral process viral process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus positive regulation of biological process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression nucleobase-containing compound biosynthetic process DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling DNA cytosine deamination DNA metabolic process DNA deamination DNA modification negative regulation of viral genome replication viral life cycle regulation of viral life cycle viral genome replication regulation of viral genome replication regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus regulation of response to stress positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA biosynthetic process regulation of primary metabolic process regulation of RNA metabolic process viral RNA genome replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex apolipoprotein B mRNA editing enzyme complex catalytic complex mRNA editing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle cytoplasmic ribonucleoprotein granule cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle protein-containing complex apolipoprotein B mRNA editing enzyme complex catalytic complex mRNA editing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex P-body ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L	IPR000475	Retroviral Vif (Viral infectivity) protein	Family
B, E, H, K	IPR003417	Core-binding factor, beta subunit	Family
B, E, H, K	IPR036552	Core-binding factor, beta subunit superfamily	Homologous Superfamily
A, D, G, J	IPR050610	APOBEC Cytidine Deaminase	Family
A, D, G, J	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, D, G, J	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, D, G, J	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E, H, K	Pharos: Q13951	acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma medulloblastoma osteosarcoma ulcerative colitis amyotrophic lateral sclerosis cancer Down syndrome IgA glomerulonephritis
A, D, G, J	Pharos: Q8IUX4	atypical teratoid rhabdoid tumor malignant glioma osteosarcoma cutaneous lupus erythematosus malignant mesothelioma plasma cell myeloma large cell medulloblastoma medulloblastoma

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.