6VAF | pdb_00006vaf

Structure of mono-ubiquitinated FANCD2 bound to non-ubiquitinated FANCI and to DNA

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)
C [auth D]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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	FANCI_S1	e6vafA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: FANCI_S1	ECOD (1.6)
B	FancD2	e6vafB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: FancD2	ECOD (1.6)
C [auth D]	ubiquitin_1	e6vafD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14674	FANCI solenoid 1 cap (FANCI_S1-cap)	FANCI solenoid 1 cap	-	Repeat
A	PF14675	FANCI solenoid 1 (FANCI_S1)	FANCI solenoid 1	-	Repeat
A	PF14676	FANCI solenoid 2 (FANCI_S2)	FANCI solenoid 2	-	Repeat
A	PF14677	FANCI solenoid 3 (FANCI_S3)	FANCI solenoid 3	-	Repeat
A	PF14678	FANCI solenoid 4 (FANCI_S4)	FANCI solenoid 4	-	Repeat
A	PF14679	FANCI helical domain 1 (FANCI_HD1)	FANCI helical domain 1	-	Repeat
C [auth D]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Fanconi anemia, complementation group I	DNA binding binding nucleic acid binding protein binding DNA polymerase binding enzyme binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process interstrand cross-link repair macromolecule metabolic process DNA repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process interstrand cross-link repair macromolecule metabolic process DNA repair regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure membrane protein-containing complex catalytic complex DNA repair complex intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure membrane protein-containing complex catalytic complex DNA repair complex intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
B	Fanconi anemia group D2 protein	protein binding binding DNA polymerase binding enzyme binding	sexual reproduction reproductive process multicellular organismal reproductive process gamete generation regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress sexual reproduction reproductive process multicellular organismal reproductive process gamete generation regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress regulation of response to stress inflammatory response multicellular organismal process regulation of leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte activation lymphocyte differentiation regulation of cell development leukocyte activation regulation of T cell differentiation multicellular organism development T cell activation cell differentiation anatomical structure development T cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of regulatory T cell differentiation cell activation regulation of T cell activation immune system process regulatory T cell differentiation regulation of hemopoiesis cellular process leukocyte differentiation regulation of lymphocyte activation cellular response to stimulus regulation of signaling cell surface receptor signaling pathway signaling regulation of signal transduction cell communication regulation of CD40 signaling pathway regulation of cell communication CD40 signaling pathway signal transduction head development brain morphogenesis animal organ development brain development nervous system development anatomical structure morphogenesis central nervous system development animal organ morphogenesis system development response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response metabolic process interstrand cross-link repair macromolecule metabolic process DNA repair DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition cell cycle mitotic intra-S DNA damage checkpoint signaling regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage meiotic chromosome segregation meiotic cell cycle organelle fission chromosome organization meiotic cell cycle process cellular component organization chromosome organization involved in meiotic cell cycle nuclear division organelle organization meiosis I meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation meiotic nuclear division homologous chromosome segregation cellular component organization or biogenesis chromosome segregation homologous recombination reciprocal homologous recombination double-strand break repair DNA recombination reciprocal meiotic recombination double-strand break repair involved in meiotic recombination response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to oxidative stress cellular response to chemical stress neuronal stem cell population maintenance maintenance of cell number stem cell population maintenance	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 organelle membraneless organelle nuclear lumen 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 organelle membraneless organelle nuclear lumen chromosome condensed chromosome protein-containing complex catalytic complex DNA repair complex cytoplasm cytosol nuclear body nucleoplasm chromatin
C [auth D]	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
D [auth S]	DNA (29-MER)	-	-	-
E [auth T]	DNA (29-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029313	FANCI solenoid 3 domain	Domain
A	IPR029310	FANCI helical domain 1	Domain
A	IPR029315	FANCI solenoid 2 domain	Domain
A	IPR029314	FANCI solenoid 4 domain	Domain
A	IPR029312	FANCI helical domain 2	Domain
A	IPR026171	Fanconi anemia group I protein	Family
A	IPR029305	FANCI solenoid 1 cap	Domain
A	IPR029308	FANCI solenoid 1 domain	Domain
B	IPR029448	Fanconi anaemia protein FANCD2	Family
C [auth D]	IPR019954	Ubiquitin conserved site	Conserved Site
C [auth D]	IPR000626	Ubiquitin-like domain	Domain
C [auth D]	IPR019956	Ubiquitin domain	Domain
C [auth D]	IPR050158	Ubiquitin and ubiquitin-like	Family
C [auth D]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NVI1	Fanconi anemia Fanconi anemia complementation group I IgA glomerulonephritis invasive ductal breast carcinoma lung cancer malignant glioma adrenal cortex carcinoma medulloblastoma atopic eczema non-small cell lung carcinoma breast cancer pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma Cytopenia primitive neuroectodermal tumor Fanconi anemia Fanconi anemia complementation group I IgA glomerulonephritis invasive ductal breast carcinoma lung cancer malignant glioma adrenal cortex carcinoma medulloblastoma atopic eczema non-small cell lung carcinoma breast cancer pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma Cytopenia primitive neuroectodermal tumor Sjogren syndrome hematopoietic and lymphoid system neoplasm inherited aplastic anemia large cell medulloblastoma malignant colon neoplasm malignant mesothelioma anemia nasopharyngeal carcinoma attention deficit hyperactivity disorder, inattentive type ovarian cancer peripheral nervous system disease breast carcinoma pituitary cancer ductal breast carcinoma in situ psoriasis esophageal atresia/tracheoesophageal fistula ulcerative colitis glioblastoma hepatocellular carcinoma intellectual disability lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm aplastic anemia neurofibromatosis type 1 atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy congenital anemia endometriosis head and neck cancer
B	Pharos: Q9BXW9	Fanconi anemia Fanconi anemia complementation group D2 intellectual disability leukemia neurofibromatosis type 1 ovarian cancer acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia aplastic anemia psoriasis congenital anemia endometriosis glioblastoma hepatocellular carcinoma invasive ductal breast carcinoma Fanconi anemia Fanconi anemia complementation group D2 intellectual disability leukemia neurofibromatosis type 1 ovarian cancer acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia aplastic anemia psoriasis congenital anemia endometriosis glioblastoma hepatocellular carcinoma invasive ductal breast carcinoma malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma adrenal cortex carcinoma Primary microcephaly atopic eczema Fanconi anemia complementation group A head and neck cancer inherited aplastic anemia large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm anemia primitive neuroectodermal tumor atypical teratoid rhabdoid tumor ductal breast carcinoma in situ esophageal atresia/tracheoesophageal fistula hematopoietic and lymphoid system neoplasm
C [auth D]	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm 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.