General information
PDB ID 6VEN
Title YEAST COMPASS IN COMPLEX WITH A UBIQUITINATED NUCLEOSOME
PDB header TRANSFERASE/STRUCTURAL PROTEIN/DNA
Date 2020-01-02
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.37
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, HOMO SAPIENS, SACCHAROMYCES CEREVISIAE
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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:
pdb6ven.pdb ABCDEFGHKLMNOPQR IJ 0
Biounits:
6ven.pdb1.pdb ABCDEFGHKLMNOPQR 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_2-132 3.3e-40 1 CL0012 A 1 131 IJ  H-Bb H-Mj L-Bb 
CENP-T_C Domain P62799_26-99 4.6e-08 1 CL0012 B 25 98 IJ  L-Bb 
Histone Domain P06897_13-91 9.5e-16 1 CL0012 C 15 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 6.7e-22 1 CL0012 D 31 101 IJ  H-Bb L-Bb 
Histone Domain P84233_39-132 2.3e-39 1 CL0012 E 38 131 IJ  H-Bb H-Mj L-Bb 
CENP-T_C Domain P62799_26-99 4.4e-08 1 CL0012 F 25 98 IJ  L-Bb 
Histone Domain P06897_13-91 6.8e-16 1 CL0012 G 13 90 IJ  H-Bb L-Bb 
Histone Domain P02281_33-102 6.9e-22 1 CL0012 H 31 101 IJ  H-Bb L-Bb 
ubiquitin Domain P0CG48_611-682 5.2e-35 1 CL0072 K 3 74   
N-SET Domain P38827_803-932 4.9e-08 1 No_clan N 849 932   
Histone_H2A_C Family P06897_92-119 2.8e-16 1 No_clan C 91 117   
Histone_H2A_C Family P06897_92-119 3.1e-17 1 No_clan G 91 118   
SET Family P38827_949-1055 1e-19 1 No_clan N 949 1055   
Dpy-30 Motif Q03323_121-161 2.1e-18 1 CL0068 P 121 161   
Dpy-30 Motif Q03323_127-161 1.8e-05 1 CL0068 Q 127 161   
WD40 Repeat P38123_44-82 1.4e-06 1 CL0186 L 86 124   
WD40 Repeat P39706_62-100 9.8e-08 1 CL0186 M 62 100   
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=1-76 C cytoplasm
K=1-76 C cytosol
K=1-76 C endocytic vesicle membrane
K=1-76 C endoplasmic reticulum membrane
K=1-76 C endosome membrane
K=1-76 C extracellular exosome
K=1-76 C extracellular space
K=1-76 C host cell
K=1-76 C mitochondrial outer membrane
K=1-76 C nucleoplasm
K=1-76 C nucleus
K=1-76 C plasma membrane
K=1-76 C vesicle
K=1-76 F protease binding
K=1-76 F protein tag
K=1-76 F RNA binding
K=1-76 F ubiquitin protein ligase binding
K=1-76 P activation of MAPK activity
K=1-76 P anaphase-promoting complex-dependent catabolic process
K=1-76 P cellular protein metabolic process
K=1-76 P cytokine-mediated signaling pathway
K=1-76 P DNA damage response, detection of DNA damage
K=1-76 P endosomal transport
K=1-76 P error-free translesion synthesis
K=1-76 P error-prone translesion synthesis
K=1-76 P global genome nucleotide-excision repair
K=1-76 P I-kappaB kinase/NF-kappaB signaling
K=1-76 P interleukin-1-mediated signaling pathway
K=1-76 P interstrand cross-link repair
K=1-76 P intracellular transport of virus
K=1-76 P JNK cascade
K=1-76 P membrane organization
K=1-76 P modification-dependent protein catabolic process
K=1-76 P MyD88-dependent toll-like receptor signaling pathway
K=1-76 P MyD88-independent toll-like receptor signaling pathway
K=1-76 P negative regulation of apoptotic process
K=1-76 P negative regulation of transcription by RNA polymerase II
K=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
K=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
K=1-76 P nucleotide-excision repair, DNA damage recognition
K=1-76 P nucleotide-excision repair, DNA duplex unwinding
K=1-76 P nucleotide-excision repair, DNA gap filling
K=1-76 P nucleotide-excision repair, DNA incision
K=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
K=1-76 P nucleotide-excision repair, preincision complex assembly
K=1-76 P positive regulation of apoptotic process
K=1-76 P positive regulation of NF-kappaB transcription factor activity
K=1-76 P positive regulation of transcription by RNA polymerase II
K=1-76 P protein deubiquitination
K=1-76 P protein polyubiquitination
K=1-76 P protein targeting to peroxisome
K=1-76 P protein ubiquitination
K=1-76 P regulation of mRNA stability
K=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
K=1-76 P stress-activated MAPK cascade
K=1-76 P transcription-coupled nucleotide-excision repair
K=1-76 P transforming growth factor beta receptor signaling pathway
K=1-76 P translesion synthesis
K=1-76 P transmembrane transport
K=1-76 P TRIF-dependent toll-like receptor signaling pathway
K=1-76 P viral life cycle
K=1-76 P virion assembly
K=1-76 P Wnt signaling pathway
L=1-315 C chromosome, telomeric region
L=1-315 C nucleus
L=1-315 C Set1C/COMPASS complex
L=1-315 F histone binding
L=1-315 P chromatin silencing at telomere
L=1-315 P histone H3-K4 methylation
L=1-315 P regulation of meiotic DNA double-strand break formation
L=1-315 P telomere maintenance
M=1-426 C chromosome, telomeric region
M=1-426 C Set1C/COMPASS complex
M=1-426 P chromatin silencing at telomere
M=1-426 P histone H3-K4 methylation
M=1-426 P regulation of transcription, DNA-templated
M=1-426 P telomere maintenance
N=762-1080 C chromosome, telomeric region
N=762-1080 C Set1C/COMPASS complex
N=762-1080 F histone methyltransferase activity (H3-K4 specific)
N=762-1080 F protein-lysine N-methyltransferase activity
N=762-1080 F RNA binding
N=762-1080 P ascospore formation
N=762-1080 P chromatin silencing at telomere
N=762-1080 P gene silencing
N=762-1080 P histone H3-K4 dimethylation
N=762-1080 P histone H3-K4 methylation
N=762-1080 P histone H3-K4 monomethylation
N=762-1080 P histone H3-K4 trimethylation
N=762-1080 P meiotic DNA double-strand break formation
N=762-1080 P negative regulation of gene expression
N=762-1080 P negative regulation of histone H4 acetylation
N=762-1080 P negative regulation of transcription by RNA polymerase II
N=762-1080 P peptidyl-lysine dimethylation
N=762-1080 P positive regulation of histone acetylation
N=762-1080 P positive regulation of synaptonemal complex assembly
N=762-1080 P positive regulation of transcription by RNA polymerase II
N=762-1080 P protein methylation
N=762-1080 P rDNA heterochromatin assembly
N=762-1080 P regulation of chromatin organization
N=762-1080 P regulation of meiotic DNA double-strand break formation
N=762-1080 P regulation of transcription from RNA polymerase II promoter in response to stress
N=762-1080 P silent mating-type cassette heterochromatin assembly
N=762-1080 P sterol homeostasis
N=762-1080 P synaptonemal complex assembly
N=762-1080 P telomere maintenance
O=1-505 C chromosome, telomeric region
O=1-505 C Set1C/COMPASS complex
O=1-505 F transcription regulatory region sequence-specific DNA binding
O=1-505 P chromatin silencing at telomere
O=1-505 P histone H3-K4 methylation
O=1-505 P histone H3-K4 trimethylation
O=1-505 P telomere maintenance
P/Q=1-175 C chromosome, telomeric region
P/Q=1-175 C MLL3/4 complex
P/Q=1-175 C Set1C/COMPASS complex
P/Q=1-175 P chromatin silencing at telomere
P/Q=1-175 P histone H3-K4 methylation
R=2-353 C chromosome, telomeric region
R=2-353 C cytosol
R=2-353 C nucleus
R=2-353 C Set1C/COMPASS complex
R=2-353 F chromatin binding
R=2-353 F metal ion binding
R=2-353 F methylated histone binding
R=2-353 P chromatin silencing at telomere
R=2-353 P histone H3-K4 methylation
R=2-353 P positive regulation of transcription, DNA-templated
R=2-353 P regulation of meiotic DNA double-strand break formation
R=2-353 P regulation of transcription, DNA-templated
Sequences
Download file with secondary structure created by Stride  
6ven.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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O (protein): 
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P (protein): 
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Q (protein): 
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R (protein): 
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