General information
PDB ID 6VAF
Title STRUCTURE OF MONO-UBIQUITINATED FANCD2 BOUND TO NON-UBIQUITINATED FANCI AND TO DNA
PDB header DNA BINDING PROTEIN/DNA
Date 2019-12-17
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.9
Kind dna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6vaf.pdb ABD ST 0
Biounits:
6vaf.pdb1.pdb ABD ST 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
ubiquitin Domain P0CG48_611-682 5.5e-35 1 CL0072 D 3 74   
FANCI_S4 Family Q9NVI1_1045-1296 4.6e-91 1 No_clan A 1045 1296 S  H-Bb 
FANCI_HD2 Family Q9NVI1_575-786 3.2e-78 1 No_clan A 545 786   
FANCI_S3 Family Q9NVI1_804-1032 1.8e-77 1 No_clan A 804 1032   
FANCI_S1 Family Q9NVI1_62-280 9.9e-70 1 No_clan A 62 280   
FANCI_S2 Family Q9NVI1_378-541 4e-60 1 No_clan A 378 541   
FANCI_HD1 Family Q9NVI1_284-370 1.4e-30 1 No_clan A 284 370   
FANCI_S1-cap Family Q9NVI1_1-53 1.2e-25 1 No_clan A 1 53   
FancD2 Family Q9BXW9_261-731 2.9e-260 1 No_clan B 311 917   
FancD2 Family Q9BXW9_732-1155 4.4e-223 1 No_clan B 840 1400   
FancD2 Family Q9BXW9_2-262 8.2e-139 1 No_clan B 45 340   
FANCI_S2 Family Q9BXW9_370-498 7.1e-05 0 No_clan B 416 579   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
B=1-1451 C condensed chromosome
B=1-1451 C cytosol
B=1-1451 C nuclear body
B=1-1451 C nucleolus
B=1-1451 C nucleoplasm
B=1-1451 C nucleus
B=1-1451 F DNA polymerase binding
B=1-1451 P brain morphogenesis
B=1-1451 P cellular response to oxidative stress
B=1-1451 P double-strand break repair involved in meiotic recombination
B=1-1451 P gamete generation
B=1-1451 P interstrand cross-link repair
B=1-1451 P intra-S DNA damage checkpoint
B=1-1451 P neuronal stem cell population maintenance
B=1-1451 P regulation of CD40 signaling pathway
B=1-1451 P regulation of DNA-binding transcription factor activity
B=1-1451 P regulation of inflammatory response
B=1-1451 P regulation of regulatory T cell differentiation
B=1-1451 P response to gamma radiation
B=1-1451 P synapsis
D=1-76 C cytoplasm
D=1-76 C cytosol
D=1-76 C endocytic vesicle membrane
D=1-76 C endoplasmic reticulum membrane
D=1-76 C endosome membrane
D=1-76 C extracellular exosome
D=1-76 C extracellular space
D=1-76 C host cell
D=1-76 C mitochondrial outer membrane
D=1-76 C nucleoplasm
D=1-76 C nucleus
D=1-76 C plasma membrane
D=1-76 C vesicle
D=1-76 F protease binding
D=1-76 F protein tag
D=1-76 F RNA binding
D=1-76 F ubiquitin protein ligase binding
D=1-76 P activation of MAPK activity
D=1-76 P anaphase-promoting complex-dependent catabolic process
D=1-76 P cellular protein metabolic process
D=1-76 P cytokine-mediated signaling pathway
D=1-76 P DNA damage response, detection of DNA damage
D=1-76 P endosomal transport
D=1-76 P error-free translesion synthesis
D=1-76 P error-prone translesion synthesis
D=1-76 P global genome nucleotide-excision repair
D=1-76 P I-kappaB kinase/NF-kappaB signaling
D=1-76 P interleukin-1-mediated signaling pathway
D=1-76 P interstrand cross-link repair
D=1-76 P intracellular transport of virus
D=1-76 P JNK cascade
D=1-76 P membrane organization
D=1-76 P modification-dependent protein catabolic process
D=1-76 P MyD88-dependent toll-like receptor signaling pathway
D=1-76 P MyD88-independent toll-like receptor signaling pathway
D=1-76 P negative regulation of apoptotic process
D=1-76 P negative regulation of transcription by RNA polymerase II
D=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
D=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
D=1-76 P nucleotide-excision repair, DNA damage recognition
D=1-76 P nucleotide-excision repair, DNA duplex unwinding
D=1-76 P nucleotide-excision repair, DNA gap filling
D=1-76 P nucleotide-excision repair, DNA incision
D=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
D=1-76 P nucleotide-excision repair, preincision complex assembly
D=1-76 P positive regulation of apoptotic process
D=1-76 P positive regulation of NF-kappaB transcription factor activity
D=1-76 P positive regulation of transcription by RNA polymerase II
D=1-76 P protein deubiquitination
D=1-76 P protein polyubiquitination
D=1-76 P protein targeting to peroxisome
D=1-76 P protein ubiquitination
D=1-76 P regulation of mRNA stability
D=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
D=1-76 P stress-activated MAPK cascade
D=1-76 P transcription-coupled nucleotide-excision repair
D=1-76 P transforming growth factor beta receptor signaling pathway
D=1-76 P translesion synthesis
D=1-76 P transmembrane transport
D=1-76 P TRIF-dependent toll-like receptor signaling pathway
D=1-76 P viral life cycle
D=1-76 P virion assembly
D=1-76 P Wnt signaling pathway
Sequences
Download file with secondary structure created by Stride  
6vaf.pdb1.pdb:   [ download sequences in FASTA format ]
S (dna): 
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T (dna): 
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A (protein): 
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B (protein): 
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D (protein): 
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