General information
PDB ID 6JMA
Title CRYO-EM STRUCTURE OF DOT1L BOUND TO H2B UBIQUITINATED NUCLEOSOME
PDB header GENE REGULATION
Date 2019-03-07
Experimental method ELECTRON MICROSCOPY
Resolution (A) 6.8
Kind dna
Organism SYNTHETIC CONSTRUCT, XENOPUS LAEVIS, 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:
pdb6jma.pdb ABCDEFGHXY IJ 0
Biounits:
6jma.pdb1.pdb ABCDEFGHXY 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 3.7e-46 1 CL0012 A 38 131 IJ   
CENP-T_C Domain P62799_26-99 4.7e-08 1 CL0012 B 25 98 IJ   
Histone Domain Q6AZJ8_15-91 9.4e-16 1 CL0012 C 14 90 IJ   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 D 29 98 IJ   
Histone Domain P84233_37-132 3.7e-46 1 CL0012 E 38 131 IJ   
CENP-T_C Domain P62799_18-99 5.2e-08 1 CL0012 F 20 98 IJ   
Histone Domain Q6AZJ8_15-91 9.2e-16 1 CL0012 G 14 90 IJ   
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 IJ   
DOT1 Domain Q8TEK3_115-317 9e-84 1 CL0063 X 115 317   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 Y 3 74   
Histone_H2A_C Family Q6AZJ8_92-119 8.1e-19 1 No_clan C 91 120   
Histone_H2A_C Family Q6AZJ8_92-119 4e-18 1 No_clan G 91 119   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=39-136 C nucleoplasm
A/E=39-136 C nucleosome
A/E=39-136 F DNA binding
A/E=39-136 F protein heterodimerization activity
B/F=17-103 C host cell nucleus
B/F=17-103 C nucleosome
B/F=17-103 C nucleus
B/F=17-103 F DNA binding
B/F=17-103 F protein heterodimerization activity
B/F=17-103 P DNA-templated transcription, initiation
D/H=34-126 C nucleosome
D/H=34-126 C nucleus
D/H=34-126 F DNA binding
D/H=34-126 F protein heterodimerization activity
X=5-332 C chromosome, telomeric region
X=5-332 C intracellular membrane-bounded organelle
X=5-332 C nucleoplasm
X=5-332 C nucleus
X=5-332 C protein-containing complex
X=5-332 F DNA binding
X=5-332 F histone methyltransferase activity
X=5-332 F histone methyltransferase activity (H3-K79 specific)
X=5-332 F histone-lysine N-methyltransferase activity
X=5-332 F transcription factor binding
X=5-332 P chromatin silencing at telomere
X=5-332 P DNA damage checkpoint
X=5-332 P DNA repair
X=5-332 P histone H3-K79 methylation
X=5-332 P positive regulation of cell population proliferation
X=5-332 P positive regulation of transcription by RNA polymerase II
X=5-332 P regulation of receptor signaling pathway via JAK-STAT
X=5-332 P regulation of transcription regulatory region DNA binding
X=5-332 P telomere organization
Y=1-76 C cytoplasm
Y=1-76 C cytosol
Y=1-76 C endocytic vesicle membrane
Y=1-76 C endoplasmic reticulum membrane
Y=1-76 C endosome membrane
Y=1-76 C extracellular exosome
Y=1-76 C extracellular space
Y=1-76 C host cell
Y=1-76 C mitochondrial outer membrane
Y=1-76 C mitochondrion
Y=1-76 C neuron projection
Y=1-76 C neuronal cell body
Y=1-76 C nucleoplasm
Y=1-76 C nucleus
Y=1-76 C plasma membrane
Y=1-76 C vesicle
Y=1-76 F protein tag
Y=1-76 F ubiquitin protein ligase binding
Y=1-76 P activation of MAPK activity
Y=1-76 P anaphase-promoting complex-dependent catabolic process
Y=1-76 P cellular protein metabolic process
Y=1-76 P cytokine-mediated signaling pathway
Y=1-76 P DNA damage response, detection of DNA damage
Y=1-76 P endosomal transport
Y=1-76 P energy homeostasis
Y=1-76 P error-free translesion synthesis
Y=1-76 P error-prone translesion synthesis
Y=1-76 P fat pad development
Y=1-76 P female gonad development
Y=1-76 P female meiosis I
Y=1-76 P global genome nucleotide-excision repair
Y=1-76 P hypothalamus gonadotrophin-releasing hormone neuron development
Y=1-76 P I-kappaB kinase/NF-kappaB signaling
Y=1-76 P interleukin-1-mediated signaling pathway
Y=1-76 P interstrand cross-link repair
Y=1-76 P intracellular transport of virus
Y=1-76 P JNK cascade
Y=1-76 P male meiosis I
Y=1-76 P membrane organization
Y=1-76 P mitochondrion transport along microtubule
Y=1-76 P modification-dependent protein catabolic process
Y=1-76 P MyD88-dependent toll-like receptor signaling pathway
Y=1-76 P MyD88-independent toll-like receptor signaling pathway
Y=1-76 P negative regulation of apoptotic process
Y=1-76 P negative regulation of transcription by RNA polymerase II
Y=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
Y=1-76 P neuron projection morphogenesis
Y=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
Y=1-76 P nucleotide-excision repair, DNA damage recognition
Y=1-76 P nucleotide-excision repair, DNA duplex unwinding
Y=1-76 P nucleotide-excision repair, DNA gap filling
Y=1-76 P nucleotide-excision repair, DNA incision
Y=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
Y=1-76 P nucleotide-excision repair, preincision complex assembly
Y=1-76 P positive regulation of apoptotic process
Y=1-76 P positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
Y=1-76 P positive regulation of NF-kappaB transcription factor activity
Y=1-76 P positive regulation of protein monoubiquitination
Y=1-76 P positive regulation of protein ubiquitination
Y=1-76 P positive regulation of transcription by RNA polymerase II
Y=1-76 P protein deubiquitination
Y=1-76 P protein polyubiquitination
Y=1-76 P protein targeting to peroxisome
Y=1-76 P protein ubiquitination
Y=1-76 P regulation of mitochondrial membrane potential
Y=1-76 P regulation of mRNA stability
Y=1-76 P regulation of neuron death
Y=1-76 P regulation of proteasomal protein catabolic process
Y=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
Y=1-76 P seminiferous tubule development
Y=1-76 P stress-activated MAPK cascade
Y=1-76 P transcription-coupled nucleotide-excision repair
Y=1-76 P transforming growth factor beta receptor signaling pathway
Y=1-76 P translesion synthesis
Y=1-76 P transmembrane transport
Y=1-76 P TRIF-dependent toll-like receptor signaling pathway
Y=1-76 P viral life cycle
Y=1-76 P virion assembly
Y=1-76 P Wnt signaling pathway
Sequences
Download file with secondary structure created by Stride  
6jma.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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X (protein): 
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Y (protein): 
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