General information
PDB ID 5KGF
Title STRUCTURAL MODEL OF 53BP1 BOUND TO A UBIQUITYLATED AND METHYLATED NUCLEOSOME, AT 4.5 A RESOLUTION
PDB header STRUCTURAL PROTEIN/DNA
Date 2016-06-13
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.54
Kind dna
Organism XENOPUS LAEVIS, HOMO SAPIENS, SYNTHETIC CONSTRUCT
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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:
pdb5kgf.pdb ABCDEFGHLOMK IJ 0
Biounits:
5kgf.pdb1.pdb ABCDEFGHLOMK IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P84233_37-132 5e-47 1 CL0012 A 35 131 IJ   
CENP-T_C Domain P62799_18-99 4.9e-08 1 CL0012 B 25 98 IJ   
Histone Domain P0C0S8_10-91 5.5e-16 1 CL0012 C 9 90 IJ   
Histone Domain P62807_27-102 4.9e-23 1 CL0012 D 23 98 IJ   
Histone Domain P84233_37-132 7.3e-47 1 CL0012 E 36 131 IJ   
CENP-T_C Domain P62799_18-99 4.9e-08 1 CL0012 F 25 98 IJ   
Histone Domain P0C0S8_10-91 5.5e-16 1 CL0012 G 9 90 IJ   
Histone Domain P62807_33-102 2.6e-22 1 CL0012 H 26 98 IJ   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 M 3 74   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 O 3 74   
Histone_H2A_C Family P0C0S8_92-122 5.2e-19 1 No_clan C 91 121   
Histone_H2A_C Family P0C0S8_92-122 5.2e-19 1 No_clan G 91 121   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-136 C nucleoplasm
A/E=1-136 C nucleosome
A/E=1-136 F DNA binding
A/E=1-136 F protein heterodimerization activity
B/F=1-103 C host cell nucleus
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 F DNA binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 P DNA-templated transcription, initiation
C/G=1-130 C extracellular exosome
C/G=1-130 C nuclear chromatin
C/G=1-130 C nucleosome
C/G=1-130 C nucleus
C/G=1-130 F DNA binding
C/G=1-130 F enzyme binding
C/G=1-130 F protein heterodimerization activity
C/G=1-130 P chromatin organization
C/G=1-130 P chromatin silencing
D/H=1-126 C cytosol
D/H=1-126 C extracellular exosome
D/H=1-126 C extracellular space
D/H=1-126 C nucleoplasm
D/H=1-126 C nucleosome
D/H=1-126 C nucleus
D/H=1-126 F DNA binding
D/H=1-126 F identical protein binding
D/H=1-126 F protein heterodimerization activity
D/H=1-126 P antibacterial humoral response
D/H=1-126 P antimicrobial humoral immune response mediated by antimicrobial peptide
D/H=1-126 P defense response to Gram-positive bacterium
D/H=1-126 P innate immune response in mucosa
D/H=1-126 P nucleosome assembly
D/H=1-126 P protein ubiquitination
K/L=1611-1631 C condensed chromosome kinetochore
K/L=1611-1631 C cytoplasm
K/L=1611-1631 C DNA repair complex
K/L=1611-1631 C nuclear body
K/L=1611-1631 C nuclear chromosome, telomeric region
K/L=1611-1631 C nucleoplasm
K/L=1611-1631 C nucleus
K/L=1611-1631 C replication fork
K/L=1611-1631 C site of double-strand break
K/L=1611-1631 F damaged DNA binding
K/L=1611-1631 F histone binding
K/L=1611-1631 F methylated histone binding
K/L=1611-1631 F p53 binding
K/L=1611-1631 F RNA polymerase II activating transcription factor binding
K/L=1611-1631 F telomeric DNA binding
K/L=1611-1631 F transcription coregulator activity
K/L=1611-1631 F ubiquitin modification-dependent histone binding
K/L=1611-1631 P cellular response to DNA damage stimulus
K/L=1611-1631 P cellular response to X-ray
K/L=1611-1631 P DNA damage checkpoint
K/L=1611-1631 P double-strand break repair via nonhomologous end joining
K/L=1611-1631 P negative regulation of double-strand break repair via homologous recombination
K/L=1611-1631 P positive regulation of DNA-binding transcription factor activity
K/L=1611-1631 P positive regulation of isotype switching
K/L=1611-1631 P positive regulation of transcription by RNA polymerase II
K/L=1611-1631 P positive regulation of transcription, DNA-templated
K/L=1611-1631 P protein homooligomerization
M/O=153-228 C cytoplasm
M/O=153-228 C cytosol
M/O=153-228 C endocytic vesicle membrane
M/O=153-228 C endoplasmic reticulum membrane
M/O=153-228 C endosome membrane
M/O=153-228 C extracellular exosome
M/O=153-228 C extracellular space
M/O=153-228 C host cell
M/O=153-228 C mitochondrial outer membrane
M/O=153-228 C mitochondrion
M/O=153-228 C neuron projection
M/O=153-228 C neuronal cell body
M/O=153-228 C nucleoplasm
M/O=153-228 C nucleus
M/O=153-228 C plasma membrane
M/O=153-228 C vesicle
M/O=153-228 F protein tag
M/O=153-228 F ubiquitin protein ligase binding
M/O=153-228 P activation of MAPK activity
M/O=153-228 P anaphase-promoting complex-dependent catabolic process
M/O=153-228 P cellular protein metabolic process
M/O=153-228 P cytokine-mediated signaling pathway
M/O=153-228 P DNA damage response, detection of DNA damage
M/O=153-228 P endosomal transport
M/O=153-228 P energy homeostasis
M/O=153-228 P error-free translesion synthesis
M/O=153-228 P error-prone translesion synthesis
M/O=153-228 P fat pad development
M/O=153-228 P female gonad development
M/O=153-228 P female meiosis I
M/O=153-228 P global genome nucleotide-excision repair
M/O=153-228 P hypothalamus gonadotrophin-releasing hormone neuron development
M/O=153-228 P I-kappaB kinase/NF-kappaB signaling
M/O=153-228 P interleukin-1-mediated signaling pathway
M/O=153-228 P interstrand cross-link repair
M/O=153-228 P intracellular transport of virus
M/O=153-228 P JNK cascade
M/O=153-228 P male meiosis I
M/O=153-228 P membrane organization
M/O=153-228 P mitochondrion transport along microtubule
M/O=153-228 P modification-dependent protein catabolic process
M/O=153-228 P MyD88-dependent toll-like receptor signaling pathway
M/O=153-228 P MyD88-independent toll-like receptor signaling pathway
M/O=153-228 P negative regulation of apoptotic process
M/O=153-228 P negative regulation of transcription by RNA polymerase II
M/O=153-228 P negative regulation of transforming growth factor beta receptor signaling pathway
M/O=153-228 P neuron projection morphogenesis
M/O=153-228 P nucleotide-binding oligomerization domain containing signaling pathway
M/O=153-228 P nucleotide-excision repair, DNA damage recognition
M/O=153-228 P nucleotide-excision repair, DNA duplex unwinding
M/O=153-228 P nucleotide-excision repair, DNA gap filling
M/O=153-228 P nucleotide-excision repair, DNA incision
M/O=153-228 P nucleotide-excision repair, DNA incision, 5'-to lesion
M/O=153-228 P nucleotide-excision repair, preincision complex assembly
M/O=153-228 P positive regulation of apoptotic process
M/O=153-228 P positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
M/O=153-228 P positive regulation of NF-kappaB transcription factor activity
M/O=153-228 P positive regulation of protein monoubiquitination
M/O=153-228 P positive regulation of protein ubiquitination
M/O=153-228 P positive regulation of transcription by RNA polymerase II
M/O=153-228 P protein deubiquitination
M/O=153-228 P protein polyubiquitination
M/O=153-228 P protein targeting to peroxisome
M/O=153-228 P protein ubiquitination
M/O=153-228 P regulation of mitochondrial membrane potential
M/O=153-228 P regulation of mRNA stability
M/O=153-228 P regulation of neuron death
M/O=153-228 P regulation of proteasomal protein catabolic process
M/O=153-228 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
M/O=153-228 P seminiferous tubule development
M/O=153-228 P stress-activated MAPK cascade
M/O=153-228 P transcription-coupled nucleotide-excision repair
M/O=153-228 P transforming growth factor beta receptor signaling pathway
M/O=153-228 P translesion synthesis
M/O=153-228 P transmembrane transport
M/O=153-228 P TRIF-dependent toll-like receptor signaling pathway
M/O=153-228 P viral life cycle
M/O=153-228 P virion assembly
M/O=153-228 P Wnt signaling pathway
Sequences
Download file with secondary structure created by Stride  
5kgf.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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K (protein): 
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L (protein): 
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M (protein): 
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O (protein): 
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