General information
PDB ID 6UH5
Title STRUCTURAL BASIS OF COMPASS ECM RECOGNITION OF THE H2BUB NUCLEOSOME
PDB header TRANSFERASE/STRUCTURAL PROTEIN/DNA
Date 2019-09-26
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.5
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:
pdb6uh5.pdb ABCDEFGHKMNQRXLOP IJ 0
Biounits:
6uh5.pdb1.pdb ABCDEFGHKMNQRXLOP IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain Q92133_39-132 2.5e-45 1 CL0012 A 37 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P62799_18-99 4.7e-08 1 CL0012 B 25 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain Q6AZJ8_15-91 5.9e-16 1 CL0012 C 12 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 1.1e-21 1 CL0012 D 29 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain Q92133_39-132 4.7e-44 1 CL0012 E 40 131 IJ  H-Bb H-Mj S-Bb L-Bb L-Mn 
CENP-T_C Domain P62799_18-99 5.2e-08 1 CL0012 F 23 98 IJ  H-Bb S-Bb L-Bb 
Histone Domain Q6AZJ8_15-91 5.9e-16 1 CL0012 G 12 90 IJ  H-Bb S-Bb L-Bb 
Histone Domain P02281_33-102 1.1e-21 1 CL0012 H 29 98 IJ  H-Bb S-Bb L-Bb 
N-SET Domain Q6CIT4_772-808 1.5e-12 1 No_clan M 771 852   
N-SET Domain Q6CIT4_727-774 2e-06 0 No_clan M 726 773   
ubiquitin Domain P0CG47_155-226 5.5e-35 1 CL0072 Q 3 74   
Histone_H2A_C Family Q6AZJ8_92-119 3.1e-17 1 No_clan C 91 118   
Histone_H2A_C Family Q6AZJ8_92-119 3.1e-17 1 No_clan G 91 118   
SET Family Q6CIT4_869-975 4.1e-18 1 No_clan M 869 975   
Dpy-30 Motif Q6CPN6_86-126 2.8e-16 1 CL0068 O 86 126   
Dpy-30 Motif Q6CPN6_86-126 1.1e-06 1 CL0068 P 86 126   
WD40 Repeat Q6CLY5_59-95 3.4e-06 1 CL0186 K 59 95   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
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/H=2-126 C nucleosome
D/H=2-126 C nucleus
D/H=2-126 F DNA binding
D/H=2-126 F protein heterodimerization activity
M=726-1000 C chromosome, telomeric region
M=726-1000 C Set1C/COMPASS complex
M=726-1000 F histone methyltransferase activity (H3-K4 specific)
M=726-1000 F RNA binding
M=726-1000 P ascospore formation
M=726-1000 P chromatin silencing at telomere
M=726-1000 P histone H3-K4 dimethylation
M=726-1000 P histone H3-K4 monomethylation
M=726-1000 P histone H3-K4 trimethylation
M=726-1000 P meiotic DNA double-strand break formation
M=726-1000 P negative regulation of histone H4 acetylation
M=726-1000 P negative regulation of transcription by RNA polymerase II
M=726-1000 P positive regulation of histone acetylation
M=726-1000 P positive regulation of synaptonemal complex assembly
M=726-1000 P positive regulation of transcription by RNA polymerase II
M=726-1000 P rDNA heterochromatin assembly
M=726-1000 P regulation of meiotic DNA double-strand break formation
M=726-1000 P regulation of transcription from RNA polymerase II promoter in response to stress
M=726-1000 P silent mating-type cassette heterochromatin assembly
M=726-1000 P sterol homeostasis
M=726-1000 P synaptonemal complex assembly
M=726-1000 P telomere maintenance
Q=1-76 C cytoplasm
Q=1-76 C cytosol
Q=1-76 C endocytic vesicle membrane
Q=1-76 C endoplasmic reticulum membrane
Q=1-76 C endosome membrane
Q=1-76 C extracellular exosome
Q=1-76 C extracellular space
Q=1-76 C host cell
Q=1-76 C mitochondrial outer membrane
Q=1-76 C mitochondrion
Q=1-76 C neuron projection
Q=1-76 C neuronal cell body
Q=1-76 C nucleoplasm
Q=1-76 C nucleus
Q=1-76 C plasma membrane
Q=1-76 C vesicle
Q=1-76 F protein tag
Q=1-76 F ubiquitin protein ligase binding
Q=1-76 P activation of MAPK activity
Q=1-76 P anaphase-promoting complex-dependent catabolic process
Q=1-76 P cellular protein metabolic process
Q=1-76 P cytokine-mediated signaling pathway
Q=1-76 P DNA damage response, detection of DNA damage
Q=1-76 P endosomal transport
Q=1-76 P energy homeostasis
Q=1-76 P error-free translesion synthesis
Q=1-76 P error-prone translesion synthesis
Q=1-76 P fat pad development
Q=1-76 P female gonad development
Q=1-76 P female meiosis I
Q=1-76 P global genome nucleotide-excision repair
Q=1-76 P hypothalamus gonadotrophin-releasing hormone neuron development
Q=1-76 P I-kappaB kinase/NF-kappaB signaling
Q=1-76 P interleukin-1-mediated signaling pathway
Q=1-76 P interstrand cross-link repair
Q=1-76 P intracellular transport of virus
Q=1-76 P JNK cascade
Q=1-76 P male meiosis I
Q=1-76 P membrane organization
Q=1-76 P mitochondrion transport along microtubule
Q=1-76 P modification-dependent protein catabolic process
Q=1-76 P MyD88-dependent toll-like receptor signaling pathway
Q=1-76 P MyD88-independent toll-like receptor signaling pathway
Q=1-76 P negative regulation of apoptotic process
Q=1-76 P negative regulation of transcription by RNA polymerase II
Q=1-76 P negative regulation of transforming growth factor beta receptor signaling pathway
Q=1-76 P neuron projection morphogenesis
Q=1-76 P nucleotide-binding oligomerization domain containing signaling pathway
Q=1-76 P nucleotide-excision repair, DNA damage recognition
Q=1-76 P nucleotide-excision repair, DNA duplex unwinding
Q=1-76 P nucleotide-excision repair, DNA gap filling
Q=1-76 P nucleotide-excision repair, DNA incision
Q=1-76 P nucleotide-excision repair, DNA incision, 5'-to lesion
Q=1-76 P nucleotide-excision repair, preincision complex assembly
Q=1-76 P positive regulation of apoptotic process
Q=1-76 P positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
Q=1-76 P positive regulation of NF-kappaB transcription factor activity
Q=1-76 P positive regulation of protein monoubiquitination
Q=1-76 P positive regulation of protein ubiquitination
Q=1-76 P positive regulation of transcription by RNA polymerase II
Q=1-76 P protein deubiquitination
Q=1-76 P protein polyubiquitination
Q=1-76 P protein targeting to peroxisome
Q=1-76 P protein ubiquitination
Q=1-76 P regulation of mitochondrial membrane potential
Q=1-76 P regulation of mRNA stability
Q=1-76 P regulation of neuron death
Q=1-76 P regulation of proteasomal protein catabolic process
Q=1-76 P regulation of transcription from RNA polymerase II promoter in response to hypoxia
Q=1-76 P seminiferous tubule development
Q=1-76 P stress-activated MAPK cascade
Q=1-76 P transcription-coupled nucleotide-excision repair
Q=1-76 P transforming growth factor beta receptor signaling pathway
Q=1-76 P translesion synthesis
Q=1-76 P transmembrane transport
Q=1-76 P TRIF-dependent toll-like receptor signaling pathway
Q=1-76 P viral life cycle
Q=1-76 P virion assembly
Q=1-76 P Wnt signaling pathway
R=2-9 C nucleoplasm
R=2-9 C nucleosome
R=2-9 F DNA binding
R=2-9 F protein heterodimerization activity
Sequences
Download file with secondary structure created by Stride  
6uh5.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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X (protein): 
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