General information
PDB ID 6R92
Title CRYO-EM STRUCTURE OF NCP-THF2(+1)-UV-DDB CLASS B
PDB header DNA BINDING PROTEIN
Date 2019-04-02
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.8
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:
pdb6r92.pdb LABCDEFGHK IJ 0
Biounits:
6r92.pdb1.pdb LABCDEFGHK IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P68431_38-132 1.1e-46 1 CL0012 A 39 132 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62805_26-99 4.7e-08 1 CL0012 B 26 99 IJ  S-Bb L-Bb 
Histone Domain P04908_12-91 1.8e-16 1 CL0012 C 10 91 IJ  H-Bb S-Bb L-Bb 
Histone Domain P06899_32-102 5.7e-22 1 CL0012 D 32 102 IJ  S-Bb L-Bb 
Histone Domain P68431_38-132 1.1e-46 1 CL0012 E 39 132 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62805_26-99 4.7e-08 1 CL0012 F 26 99 IJ  S-Bb L-Bb 
Histone Domain P04908_12-91 1.8e-16 1 CL0012 G 10 91 IJ  H-Bb S-Bb L-Bb 
Histone Domain P06899_32-102 1.2e-22 1 CL0012 H 30 102 IJ  H-Bb S-Bb L-Bb 
MMS1_N Domain Q16531_75-392 2.9e-73 1 No_clan K 75 724   
Histone_H2A_C Family P04908_92-126 4e-20 1 No_clan C 92 126 IJ  L-Bb L-Mj 
Histone_H2A_C Family P04908_92-126 4e-20 1 No_clan G 92 126   
CPSF_A Repeat Q16531_788-1099 4.4e-86 1 CL0186 K 788 1099   
WD40 Repeat Q92466_232-271 6.3e-06 1 CL0186 L 232 271 J  L-Bb 
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-136 C extracellular exosome
A/E=1-136 C extracellular region
A/E=1-136 C membrane
A/E=1-136 C nuclear chromosome
A/E=1-136 C nuclear nucleosome
A/E=1-136 C nucleoplasm
A/E=1-136 C nucleosome
A/E=1-136 C nucleus
A/E=1-136 C protein-containing complex
A/E=1-136 F cadherin binding
A/E=1-136 F DNA binding
A/E=1-136 F protein heterodimerization activity
A/E=1-136 P blood coagulation
A/E=1-136 P cellular protein metabolic process
A/E=1-136 P chromatin organization
A/E=1-136 P DNA replication-dependent nucleosome assembly
A/E=1-136 P interleukin-7-mediated signaling pathway
A/E=1-136 P negative regulation of gene expression, epigenetic
A/E=1-136 P nucleosome assembly
A/E=1-136 P rDNA heterochromatin assembly
A/E=1-136 P regulation of gene silencing
A/E=1-136 P regulation of gene silencing by miRNA
A/E=1-136 P regulation of megakaryocyte differentiation
A/E=1-136 P telomere organization
B/F=1-103 C extracellular exosome
B/F=1-103 C extracellular region
B/F=1-103 C host cell nucleus
B/F=1-103 C membrane
B/F=1-103 C nuclear chromosome
B/F=1-103 C nuclear chromosome, telomeric region
B/F=1-103 C nuclear nucleosome
B/F=1-103 C nucleoplasm
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 C protein-containing complex
B/F=1-103 F DNA binding
B/F=1-103 F protein domain specific binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 F RNA binding
B/F=1-103 P cellular protein metabolic process
B/F=1-103 P CENP-A containing nucleosome assembly
B/F=1-103 P DNA replication-dependent nucleosome assembly
B/F=1-103 P DNA replication-independent nucleosome assembly
B/F=1-103 P DNA-templated transcription, initiation
B/F=1-103 P double-strand break repair via nonhomologous end joining
B/F=1-103 P negative regulation of gene expression, epigenetic
B/F=1-103 P negative regulation of megakaryocyte differentiation
B/F=1-103 P nucleosome assembly
B/F=1-103 P rDNA heterochromatin assembly
B/F=1-103 P regulation of gene silencing by miRNA
B/F=1-103 P regulation of megakaryocyte differentiation
B/F=1-103 P telomere capping
B/F=1-103 P telomere organization
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 protein heterodimerization activity
C/G=1-130 P chromatin organization
C/G=1-130 P chromatin silencing
C/G=1-130 P negative regulation of cell population proliferation
D/H=1-126 C cytosol
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 lipopolysaccharide 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-negative bacterium
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 killing of cells of other organism
D/H=1-126 P negative regulation of tumor necrosis factor-mediated signaling pathway
D/H=1-126 P nucleosome assembly
D/H=1-126 P protein ubiquitination
K=1-395, K=706-1140 C Cul4-RING E3 ubiquitin ligase complex
K=1-395, K=706-1140 C Cul4A-RING E3 ubiquitin ligase complex
K=1-395, K=706-1140 C Cul4B-RING E3 ubiquitin ligase complex
K=1-395, K=706-1140 C cullin-RING ubiquitin ligase complex
K=1-395, K=706-1140 C cytoplasm
K=1-395, K=706-1140 C extracellular exosome
K=1-395, K=706-1140 C extracellular space
K=1-395, K=706-1140 C nuclear chromosome, telomeric region
K=1-395, K=706-1140 C nucleoplasm
K=1-395, K=706-1140 C nucleus
K=1-395, K=706-1140 C protein-containing complex
K=1-395, K=706-1140 F cullin family protein binding
K=1-395, K=706-1140 F damaged DNA binding
K=1-395, K=706-1140 F DNA binding
K=1-395, K=706-1140 F protein-containing complex binding
K=1-395, K=706-1140 F protein-macromolecule adaptor activity
K=1-395, K=706-1140 F WD40-repeat domain binding
K=1-395, K=706-1140 P cellular response to DNA damage stimulus
K=1-395, K=706-1140 P DNA damage response, detection of DNA damage
K=1-395, K=706-1140 P DNA repair
K=1-395, K=706-1140 P global genome nucleotide-excision repair
K=1-395, K=706-1140 P histone H2A monoubiquitination
K=1-395, K=706-1140 P interaction with symbiont
K=1-395, K=706-1140 P negative regulation of apoptotic process
K=1-395, K=706-1140 P nucleotide-excision repair
K=1-395, K=706-1140 P nucleotide-excision repair, DNA damage recognition
K=1-395, K=706-1140 P nucleotide-excision repair, DNA duplex unwinding
K=1-395, K=706-1140 P nucleotide-excision repair, DNA incision
K=1-395, K=706-1140 P nucleotide-excision repair, DNA incision, 3'-to lesion
K=1-395, K=706-1140 P nucleotide-excision repair, DNA incision, 5'-to lesion
K=1-395, K=706-1140 P nucleotide-excision repair, preincision complex assembly
K=1-395, K=706-1140 P nucleotide-excision repair, preincision complex stabilization
K=1-395, K=706-1140 P positive regulation by virus of viral protein levels in host cell
K=1-395, K=706-1140 P positive regulation of gluconeogenesis
K=1-395, K=706-1140 P positive regulation of protein catabolic process
K=1-395, K=706-1140 P positive regulation of viral genome replication
K=1-395, K=706-1140 P positive regulation of viral release from host cell
K=1-395, K=706-1140 P post-translational protein modification
K=1-395, K=706-1140 P proteasomal protein catabolic process
K=1-395, K=706-1140 P proteasome-mediated ubiquitin-dependent protein catabolic process
K=1-395, K=706-1140 P protein ubiquitination
K=1-395, K=706-1140 P regulation of circadian rhythm
K=1-395, K=706-1140 P regulation of mitotic cell cycle phase transition
K=1-395, K=706-1140 P rhythmic process
K=1-395, K=706-1140 P transcription-coupled nucleotide-excision repair
K=1-395, K=706-1140 P ubiquitin-dependent protein catabolic process
K=1-395, K=706-1140 P UV-damage excision repair
K=1-395, K=706-1140 P viral process
K=1-395, K=706-1140 P Wnt signaling pathway
L=1-427 C cell junction
L=1-427 C Cul4-RING E3 ubiquitin ligase complex
L=1-427 C Cul4B-RING E3 ubiquitin ligase complex
L=1-427 C nucleoplasm
L=1-427 C nucleus
L=1-427 C protein-containing complex
L=1-427 F damaged DNA binding
L=1-427 F DNA binding
L=1-427 F protein-containing complex binding
L=1-427 P DNA repair
L=1-427 P global genome nucleotide-excision repair
L=1-427 P histone H2A monoubiquitination
L=1-427 P nucleotide-excision repair
L=1-427 P nucleotide-excision repair, DNA damage recognition
L=1-427 P nucleotide-excision repair, DNA duplex unwinding
L=1-427 P nucleotide-excision repair, DNA incision
L=1-427 P nucleotide-excision repair, DNA incision, 3'-to lesion
L=1-427 P nucleotide-excision repair, DNA incision, 5'-to lesion
L=1-427 P nucleotide-excision repair, preincision complex assembly
L=1-427 P nucleotide-excision repair, preincision complex stabilization
L=1-427 P post-translational protein modification
L=1-427 P protein autoubiquitination
L=1-427 P protein deubiquitination
L=1-427 P protein polyubiquitination
L=1-427 P pyrimidine dimer repair
L=1-427 P response to UV
L=1-427 P UV-damage excision repair
Sequences
Download file with secondary structure created by Stride  
6r92.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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