General information
PDB ID 6T9L
Title SAGA DUB MODULE BOUND TO A UBIQITINATED NUCLEOSOME
PDB header GENE REGULATION
Date 2019-10-28
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.6
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, HOMO SAPIENS
Download
complex
View in
Jmol
Quick Links
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:
pdb6t9l.pdb ABCDEFGHKLMNO IJ 0
Biounits:
6t9l.pdb1.pdb ABCDEFGHKLMNO 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 7.9e-46 1 CL0012 A 38 131 IJ   
CENP-T_C Domain P62799_18-99 4.9e-08 1 CL0012 B 25 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 28 98 IJ   
Histone Domain P84233_37-132 8.5e-45 1 CL0012 E 40 131 IJ   
CENP-T_C Domain P62799_26-99 4.2e-08 1 CL0012 F 26 98 IJ   
Histone Domain P06897_19-91 8.9e-16 1 CL0012 G 14 90 IJ   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 JI   
zf-UBP Domain P50102_46-108 5.8e-11 1 CL0229 K 46 108   
Sgf11_N Domain Q03067_6-44 8.7e-24 1 No_clan M 6 44   
zf_C2H2_13 Domain P53165_59-98 3.6e-22 1 CL0361 N 59 98   
ubiquitin Domain P0CG48_611-682 5.5e-35 1 CL0072 O 3 74   
Histone_H2A_C Family P06897_92-120 2.9e-17 1 No_clan C 91 118   
Histone_H2A_C Family P06897_92-120 3e-17 1 No_clan G 91 118   
UCH Family P50102_137-465 1.9e-61 1 CL0125 K 137 465   
EnY2 Family Q6WNK7_9-89 2.6e-25 1 No_clan L 9 89   
Sgf11 Family Q03067_67-95 3.6e-14 1 CL0361 M 67 95   
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
D=5-126 C nucleosome
D=5-126 C nucleus
D=5-126 F DNA binding
D=5-126 F protein heterodimerization activity
K=1-471 C DUBm complex
K=1-471 C SAGA complex
K=1-471 C SLIK (SAGA-like) complex
K=1-471 F molecular adaptor activity
K=1-471 F thiol-dependent ubiquitin-specific protease activity
K=1-471 F zinc ion binding
K=1-471 P histone deubiquitination
K=1-471 P histone H3-K4 methylation
K=1-471 P histone H3-K79 methylation
K=1-471 P RNA splicing
K=1-471 P ubiquitin-dependent protein catabolic process
L=1-96 C DUBm complex
L=1-96 C nuclear pore
L=1-96 C nucleoplasm
L=1-96 C P-body
L=1-96 C SAGA complex
L=1-96 C transcription export complex 2
L=1-96 F chromatin binding
L=1-96 F enzyme activator activity
L=1-96 F transcription coactivator activity
L=1-96 P histone deubiquitination
L=1-96 P histone H3-K4 methylation
L=1-96 P histone H3-K79 methylation
L=1-96 P nuclear retention of pre-mRNA at the site of transcription
L=1-96 P poly(A)+ mRNA export from nucleus
L=1-96 P positive regulation of transcription by RNA polymerase II
L=1-96 P posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
L=1-96 P regulation of protein localization
L=1-96 P regulation of transcription by RNA polymerase II
L=1-96 P transcription elongation from RNA polymerase II promoter
M=1-99 C DUBm complex
M=1-99 C nucleus
M=1-99 C SAGA complex
M=1-99 F enzyme activator activity
M=1-99 F transcription coactivator activity
M=1-99 F zinc ion binding
M=1-99 P histone deubiquitination
M=1-99 P positive regulation of transcription, DNA-templated
M=1-99 P regulation of transcription by RNA polymerase II
N=1-657 C cytosol
N=1-657 C DUBm complex
N=1-657 C nucleus
N=1-657 C SAGA complex
N=1-657 C SLIK (SAGA-like) complex
N=1-657 F enzyme activator activity
N=1-657 F structural molecule activity
N=1-657 P cellular protein-containing complex assembly
N=1-657 P chromatin organization
N=1-657 P histone acetylation
N=1-657 P histone deubiquitination
N=1-657 P mRNA export from nucleus
N=1-657 P positive regulation of RNA polymerase II transcription preinitiation complex assembly
N=1-657 P regulation of nucleocytoplasmic transport
N=1-657 P regulation of protein localization to chromatin
N=1-657 P regulation of transcription by RNA polymerase II
N=1-657 P RITS complex assembly
O=1-76 C cytoplasm
O=1-76 C cytosol
O=1-76 C endocytic vesicle membrane
O=1-76 C endoplasmic reticulum membrane
O=1-76 C endosome membrane
O=1-76 C extracellular exosome
O=1-76 C extracellular space
O=1-76 C host cell
O=1-76 C mitochondrial outer membrane
O=1-76 C nucleoplasm
O=1-76 C nucleus
O=1-76 C plasma membrane
O=1-76 C vesicle
O=1-76 F protease binding
O=1-76 F protein tag
O=1-76 F RNA binding
O=1-76 F ubiquitin protein ligase binding
O=1-76 P activation of MAPK activity
O=1-76 P anaphase-promoting complex-dependent catabolic process
O=1-76 P cellular protein metabolic process
O=1-76 P cytokine-mediated signaling pathway
O=1-76 P DNA damage response, detection of DNA damage
O=1-76 P endosomal transport
O=1-76 P error-free translesion synthesis
O=1-76 P error-prone translesion synthesis
O=1-76 P global genome nucleotide-excision repair
O=1-76 P I-kappaB kinase/NF-kappaB signaling
O=1-76 P interleukin-1-mediated signaling pathway
O=1-76 P interstrand cross-link repair
O=1-76 P intracellular transport of virus
O=1-76 P JNK cascade
O=1-76 P membrane organization
O=1-76 P modification-dependent protein catabolic process
O=1-76 P MyD88-dependent toll-like receptor signaling pathway
O=1-76 P MyD88-independent toll-like receptor signaling pathway
O=1-76 P negative regulation of apoptotic process
O=1-76 P negative regulation of transcription by RNA polymerase II
O=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
O=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
O=1-76 P nucleotide-excision repair, DNA damage recognition
O=1-76 P nucleotide-excision repair, DNA duplex unwinding
O=1-76 P nucleotide-excision repair, DNA gap filling
O=1-76 P nucleotide-excision repair, DNA incision
O=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
O=1-76 P nucleotide-excision repair, preincision complex assembly
O=1-76 P positive regulation of apoptotic process
O=1-76 P positive regulation of NF-kappaB transcription factor activity
O=1-76 P positive regulation of transcription by RNA polymerase II
O=1-76 P protein deubiquitination
O=1-76 P protein polyubiquitination
O=1-76 P protein targeting to peroxisome
O=1-76 P protein ubiquitination
O=1-76 P regulation of mRNA stability
O=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
O=1-76 P stress-activated MAPK cascade
O=1-76 P transcription-coupled nucleotide-excision repair
O=1-76 P transforming growth factor beta receptor signaling pathway
O=1-76 P translesion synthesis
O=1-76 P transmembrane transport
O=1-76 P TRIF-dependent toll-like receptor signaling pathway
O=1-76 P viral life cycle
O=1-76 P virion assembly
O=1-76 P Wnt signaling pathway
Sequences
Download file with secondary structure created by Stride  
6t9l.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
Click "SHOW" for view sequence
J (dna): 
Click "SHOW" for view sequence
A (protein): 
Click "SHOW" for view sequence
B (protein): 
Click "SHOW" for view sequence
C (protein): 
Click "SHOW" for view sequence
D (protein): 
Click "SHOW" for view sequence
E (protein): 
Click "SHOW" for view sequence
F (protein): 
Click "SHOW" for view sequence
G (protein): 
Click "SHOW" for view sequence
H (protein): 
Click "SHOW" for view sequence
K (protein): 
Click "SHOW" for view sequence
L (protein): 
Click "SHOW" for view sequence
M (protein): 
Click "SHOW" for view sequence
N (protein): 
Click "SHOW" for view sequence
O (protein): 
Click "SHOW" for view sequence
© NPIDB team 2003 - 2021

text