5W2M | pdb_00005w2m

APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
I [auth M]	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
H [auth L]	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
G [auth K]	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
F [auth J]	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8105527	3001838	SCOP2B (2022-06-29)
B	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)
I [auth M]	APOBEC_N	e5w2mM1	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)
H [auth L]	APOBEC_N	e5w2mL1	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 [auth K]	APOBEC_N	e5w2mK1	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)
F [auth J]	APOBEC_N	e5w2mJ1	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	e5w2mD1	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)
C	APOBEC_N	e5w2mC1	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)
B	APOBEC_N	e5w2mB1	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	e5w2mA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	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
E, J [auth N]	DNA (5'-D(PTPTPTPTPTPTPTPTPTPT)-3')	-	-	-
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	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
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	IPR050610	APOBEC Cytidine Deaminase	Family
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, F [auth J], A, B, C, D, F [auth J], G [auth K], H [auth L], I [auth M]	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.