General information
PDB ID 6J99
Title CRYO-EM STRUCTURE OF HUMAN DOT1L IN COMPLEX WITH AN H2B- MONOUBIQUITINATED NUCLEOSOME
PDB header TRANSCRIPTION
Date 2019-01-22
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.1
Kind dna
Organism XENOPUS LAEVIS, SYNTHETIC CONSTRUCT, 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:
pdb6j99.pdb ABCDEFGHLK IJ 0
Biounits:
6j99.pdb1.pdb ABCDEFGHLK IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain A0A310TTQ1_39-132 7.9e-46 1 CL0012 A 38 131 IJ  H-Bb H-Mj S-Bb L-Bb 
CENP-T_C Domain P62799_18-99 5e-08 1 CL0012 B 20 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain Q6AZJ8_15-91 5e-16 1 CL0012 C 11 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 4e-22 1 CL0012 D 27 98 IJ  H-Bb L-Bb L-Mn 
Histone Domain A0A310TTQ1_39-132 7.9e-46 1 CL0012 E 38 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P62799_26-99 4.6e-08 1 CL0012 F 25 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain Q6AZJ8_15-91 6.6e-16 1 CL0012 G 13 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 7.2e-22 1 CL0012 H 28 98 IJ  H-Bb H-Mj S-Bb L-Bb 
DOT1 Domain Q8TEK3_115-317 8.7e-84 1 CL0063 K 115 317   
ubiquitin Domain P62979_3-74 5.5e-35 1 CL0072 L 3 74   
Histone_H2A_C Family Q6AZJ8_92-119 3.2e-17 1 No_clan C 91 118   
Histone_H2A_C Family Q6AZJ8_92-119 2.9e-16 1 No_clan G 91 117   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
B/F=1-103 C host cell nucleus
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 F DNA binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 P DNA-templated transcription, initiation
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=1-416 C chromosome, telomeric region
K=1-416 C intracellular membrane-bounded organelle
K=1-416 C nucleoplasm
K=1-416 C nucleus
K=1-416 C protein-containing complex
K=1-416 F DNA binding
K=1-416 F histone methyltransferase activity
K=1-416 F histone methyltransferase activity (H3-K79 specific)
K=1-416 F histone-lysine N-methyltransferase activity
K=1-416 F transcription factor binding
K=1-416 P chromatin silencing at telomere
K=1-416 P DNA damage checkpoint
K=1-416 P DNA repair
K=1-416 P histone H3-K79 methylation
K=1-416 P positive regulation of cell population proliferation
K=1-416 P positive regulation of transcription by RNA polymerase II
K=1-416 P regulation of receptor signaling pathway via JAK-STAT
K=1-416 P regulation of transcription regulatory region DNA binding
K=1-416 P telomere organization
L=1-76 C cytoplasm
L=1-76 C cytosol
L=1-76 C cytosolic small ribosomal subunit
L=1-76 C endocytic vesicle membrane
L=1-76 C endoplasmic reticulum membrane
L=1-76 C endosome membrane
L=1-76 C extracellular exosome
L=1-76 C extracellular space
L=1-76 C host cell
L=1-76 C membrane
L=1-76 C mitochondrial outer membrane
L=1-76 C nucleolus
L=1-76 C nucleoplasm
L=1-76 C nucleus
L=1-76 C plasma membrane
L=1-76 C small ribosomal subunit
L=1-76 C vesicle
L=1-76 F metal ion binding
L=1-76 F protein tag
L=1-76 F RNA binding
L=1-76 F structural constituent of ribosome
L=1-76 F ubiquitin protein ligase binding
L=1-76 P activation of MAPK activity
L=1-76 P anaphase-promoting complex-dependent catabolic process
L=1-76 P cellular protein metabolic process
L=1-76 P cytokine-mediated signaling pathway
L=1-76 P DNA damage response, detection of DNA damage
L=1-76 P endosomal transport
L=1-76 P error-free translesion synthesis
L=1-76 P error-prone translesion synthesis
L=1-76 P global genome nucleotide-excision repair
L=1-76 P I-kappaB kinase/NF-kappaB signaling
L=1-76 P interleukin-1-mediated signaling pathway
L=1-76 P interstrand cross-link repair
L=1-76 P intracellular transport of virus
L=1-76 P JNK cascade
L=1-76 P membrane organization
L=1-76 P modification-dependent protein catabolic process
L=1-76 P MyD88-dependent toll-like receptor signaling pathway
L=1-76 P MyD88-independent toll-like receptor signaling pathway
L=1-76 P negative regulation of apoptotic process
L=1-76 P negative regulation of transcription by RNA polymerase II
L=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
L=1-76 P nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
L=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
L=1-76 P nucleotide-excision repair, DNA damage recognition
L=1-76 P nucleotide-excision repair, DNA duplex unwinding
L=1-76 P nucleotide-excision repair, DNA gap filling
L=1-76 P nucleotide-excision repair, DNA incision
L=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
L=1-76 P nucleotide-excision repair, preincision complex assembly
L=1-76 P positive regulation of apoptotic process
L=1-76 P positive regulation of NF-kappaB transcription factor activity
L=1-76 P positive regulation of transcription by RNA polymerase II
L=1-76 P protein deubiquitination
L=1-76 P protein polyubiquitination
L=1-76 P protein targeting to peroxisome
L=1-76 P protein ubiquitination
L=1-76 P regulation of mRNA stability
L=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
L=1-76 P SRP-dependent cotranslational protein targeting to membrane
L=1-76 P stress-activated MAPK cascade
L=1-76 P transcription-coupled nucleotide-excision repair
L=1-76 P transforming growth factor beta receptor signaling pathway
L=1-76 P translation
L=1-76 P translational initiation
L=1-76 P translesion synthesis
L=1-76 P transmembrane transport
L=1-76 P TRIF-dependent toll-like receptor signaling pathway
L=1-76 P viral life cycle
L=1-76 P viral transcription
L=1-76 P virion assembly
L=1-76 P Wnt signaling pathway
Sequences
Download file with secondary structure created by Stride  
6j99.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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