General information
PDB ID 4R8P
Title CRYSTAL STRUCTURE OF THE RING1B/BMI1/UBCH5C PRC1 UBIQUITYLATION MODULE BOUND TO THE NUCLEOSOME CORE PARTICLE
PDB header STRUCTURAL PROTEIN/DNA
Date 2014-09-02
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.28
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC DNA, 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:
pdb4r8p.pdb ABCDEFGHKLMN IJ 0
Biounits:
4r8p.pdb1.pdb ABCDEFGHKLMN 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 3.8e-46 1 CL0012 A 37 131 IJ   
CENP-T_C Domain P62799_18-99 5.2e-08 1 CL0012 B 23 98 IJ   
Histone Domain P06897_19-91 1.2e-15 1 CL0012 C 16 90 IJ   
Histone Domain P02281_33-102 7.2e-22 1 CL0012 D 31 101 IJ   
Histone Domain P84233_37-132 7.9e-46 1 CL0012 E 38 131 IJ   
CENP-T_C Domain P62799_26-99 4.7e-08 1 CL0012 F 25 98 IJ   
Histone Domain P06897_13-91 5.9e-16 1 CL0012 G 12 90 IJ   
Histone Domain P02281_33-102 7.2e-22 1 CL0012 H 31 101 IJ   
zf-C3HC4_2 Domain P35226_17-56 2.1e-11 1 CL0229 K 17 56   
UQ_con Domain P61077_5-142 3e-52 1 CL0208 L 205 342 IJ   
zf-C3HC4_2 Domain Q99496_50-90 1.7e-16 1 CL0229 L 50 90   
zf-C3HC4_2 Domain P35226_17-56 1.7e-11 1 CL0229 M 17 56   
UQ_con Domain P61077_5-142 2.9e-52 1 CL0208 N 205 342   
zf-C3HC4_2 Domain Q99496_50-90 1.7e-16 1 CL0229 N 50 90   
Histone_H2A_C Family P06897_92-120 3.8e-18 1 No_clan C 91 119   
Histone_H2A_C Family P06897_92-120 3.1e-17 1 No_clan G 91 118   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=2-136 C nucleoplasm
A/E=2-136 C nucleosome
A/E=2-136 F DNA binding
A/E=2-136 F protein heterodimerization activity
B/F=2-103 C host cell nucleus
B/F=2-103 C nucleosome
B/F=2-103 C nucleus
B/F=2-103 F DNA binding
B/F=2-103 F protein heterodimerization activity
B/F=2-103 P DNA-templated transcription, initiation
C/G=2-130 C nucleosome
C/G=2-130 C nucleus
C/G=2-130 F DNA binding
C/G=2-130 F protein heterodimerization activity
D/H=5-126 C nucleosome
D/H=5-126 C nucleus
D/H=5-126 F DNA binding
D/H=5-126 F protein heterodimerization activity
K/M=2-109 C cytosol
K/M=2-109 C nuclear body
K/M=2-109 C nucleoplasm
K/M=2-109 C nucleus
K/M=2-109 C PcG protein complex
K/M=2-109 C PRC1 complex
K/M=2-109 C ubiquitin ligase complex
K/M=2-109 F promoter-specific chromatin binding
K/M=2-109 F RING-like zinc finger domain binding
K/M=2-109 F zinc ion binding
K/M=2-109 P chromatin silencing
K/M=2-109 P hemopoiesis
K/M=2-109 P histone H2A-K119 monoubiquitination
K/M=2-109 P negative regulation of G0 to G1 transition
K/M=2-109 P negative regulation of gene expression, epigenetic
K/M=2-109 P negative regulation of transcription by RNA polymerase II
K/M=2-109 P positive regulation of fibroblast proliferation
K/M=2-109 P positive regulation of ubiquitin-protein transferase activity
K/M=2-109 P regulation of gene expression
K/M=2-109 P segment specification
L/N=2-116 C euchromatin
L/N=2-116 C MLL1 complex
L/N=2-116 C nuclear body
L/N=2-116 C nucleoplasm
L/N=2-116 C nucleus
L/N=2-116 C PcG protein complex
L/N=2-116 C PRC1 complex
L/N=2-116 C sex chromatin
L/N=2-116 C ubiquitin ligase complex
L/N=2-116 F chromatin binding
L/N=2-116 F RING-like zinc finger domain binding
L/N=2-116 F ubiquitin protein ligase activity
L/N=2-116 F zinc ion binding
L/N=2-116 P anterior/posterior axis specification
L/N=2-116 P gastrulation with mouth forming second
L/N=2-116 P gene expression
L/N=2-116 P germ cell development
L/N=2-116 P histone H2A monoubiquitination
L/N=2-116 P histone H2A-K119 monoubiquitination
L/N=2-116 P mitotic cell cycle
L/N=2-116 P negative regulation of DNA-binding transcription factor activity
L/N=2-116 P negative regulation of G0 to G1 transition
L/N=2-116 P negative regulation of transcription by RNA polymerase II
L/N=2-147 C cytosol
L/N=2-147 C endosome membrane
L/N=2-147 C extracellular exosome
L/N=2-147 C nucleoplasm
L/N=2-147 C nucleus
L/N=2-147 C plasma membrane
L/N=2-147 F ATP binding
L/N=2-147 F ubiquitin conjugating enzyme activity
L/N=2-147 F ubiquitin-protein transferase activity
L/N=2-147 P apoptotic process
L/N=2-147 P BMP signaling pathway
L/N=2-147 P cellular protein modification process
L/N=2-147 P cellular response to cadmium ion
L/N=2-147 P cellular response to mercury ion
L/N=2-147 P DNA repair
L/N=2-147 P MyD88-independent toll-like receptor signaling pathway
L/N=2-147 P negative regulation of transcription by RNA polymerase II
L/N=2-147 P positive regulation of protein targeting to mitochondrion
L/N=2-147 P proteasome-mediated ubiquitin-dependent protein catabolic process
L/N=2-147 P protein autoubiquitination
L/N=2-147 P protein K11-linked ubiquitination
L/N=2-147 P protein K48-linked ubiquitination
L/N=2-147 P protein monoubiquitination
L/N=2-147 P protein polyubiquitination
L/N=2-147 P protein targeting to peroxisome
L/N=2-147 P protein ubiquitination
L/N=2-147 P TRIF-dependent toll-like receptor signaling pathway
L/N=2-147 P ubiquitin-dependent protein catabolic process
Sequences
Download file with secondary structure created by Stride  
4r8p.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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N (protein): 
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