General information
PDB ID 6HTS
Title CRYO-EM STRUCTURE OF THE HUMAN INO80 COMPLEX BOUND TO NUCLEOSOME
PDB header DNA BINDING PROTEIN
Date 2018-10-04
Experimental method ELECTRON MICROSCOPY
Resolution (A) 4.8
Kind dna
Organism HOMO SAPIENS, SYNTHETIC CONSTRUCT
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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:
pdb6hts.pdb ABCDEFGHIJKLMNOPR XY 0
Biounits:
6hts.pdb1.pdb ABCDEFGHIJKLMNOPR XY 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
TIP49 Domain Q9Y265_14-369 7.8e-169 1 CL0023 A 14 369   
TIP49_C Domain Q9Y265_374-439 4.1e-27 1 CL0671 A 374 439   
TIP49 Domain Q9Y230_21-365 3.6e-157 1 CL0023 B 21 365   
TIP49_C Domain Q9Y230_370-435 2.2e-28 1 CL0671 B 370 435   
TIP49 Domain Q9Y265_14-369 1.7e-170 1 CL0023 C 14 369   
TIP49_C Domain Q9Y265_374-439 4.2e-27 1 CL0671 C 374 439   
TIP49 Domain Q9Y230_21-365 2.1e-160 1 CL0023 D 21 365   
TIP49_C Domain Q9Y230_370-435 2.2e-28 1 CL0671 D 370 435   
TIP49 Domain Q9Y265_14-369 1.1e-173 1 CL0023 E 14 369   
TIP49_C Domain Q9Y265_374-439 4.3e-27 1 CL0671 E 374 439   
TIP49 Domain Q9Y230_21-365 2.1e-160 1 CL0023 F 21 365   
TIP49_C Domain Q9Y230_370-435 2.2e-28 1 CL0671 F 370 435   
SNF2-rel_dom Domain Q9ULG1_521-822 7.9e-54 1 CL0023 G 521 829   
Helicase_C Domain Q9ULG1_1101-1214 1.3e-17 1 CL0023 G 1101 1214 Y   
Histone Domain P68431_39-132 9.7e-46 1 CL0012 I 40 131 XY   
CENP-T_C Domain P62805_26-99 4.7e-08 1 CL0012 J 25 98 XY   
Histone Domain P04908_16-91 3.3e-16 1 CL0012 K 13 90 XY   
Histone Domain P06899_33-102 2.3e-22 1 CL0012 L 30 101 XY   
Histone Domain P68431_39-132 4.9e-47 1 CL0012 M 37 131 XY   
CENP-T_C Domain P62805_19-99 5.2e-08 1 CL0012 N 23 98 XY   
Histone Domain P04908_16-91 4.3e-16 1 CL0012 O 14 90 XY   
Histone Domain P06899_33-102 5.5e-22 1 CL0012 P 31 101 XY   
zf-HIT Domain Q9C086_305-336 2.9e-07 1 CL0175 R 305 336   
Actin Family Q9H9F9_32-567 1.4e-41 1 CL0108 H 58 567   
Histone_H2A_C Family P04908_92-119 2.4e-17 1 No_clan K 91 118   
Histone_H2A_C Family P04908_92-119 2.4e-17 1 No_clan O 91 118   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/C/E=1-456 C cytosol
A/C/E=1-456 C extracellular exosome
A/C/E=1-456 C Ino80 complex
A/C/E=1-456 C membrane
A/C/E=1-456 C microtubule organizing center
A/C/E=1-456 C MLL1 complex
A/C/E=1-456 C NuA4 histone acetyltransferase complex
A/C/E=1-456 C nuclear matrix
A/C/E=1-456 C nucleoplasm
A/C/E=1-456 C nucleus
A/C/E=1-456 C R2TP complex
A/C/E=1-456 C ribonucleoprotein complex
A/C/E=1-456 C Swr1 complex
A/C/E=1-456 F 5'-3' DNA helicase activity
A/C/E=1-456 F ADP binding
A/C/E=1-456 F ATP binding
A/C/E=1-456 F ATPase activity
A/C/E=1-456 F ATPase binding
A/C/E=1-456 F cadherin binding
A/C/E=1-456 F DNA helicase activity
A/C/E=1-456 F TBP-class protein binding
A/C/E=1-456 F TFIID-class transcription factor complex binding
A/C/E=1-456 F transcription coactivator activity
A/C/E=1-456 P beta-catenin-TCF complex assembly
A/C/E=1-456 P box C/D snoRNP assembly
A/C/E=1-456 P cell cycle
A/C/E=1-456 P cell division
A/C/E=1-456 P CENP-A containing nucleosome assembly
A/C/E=1-456 P chromatin remodeling
A/C/E=1-456 P DNA recombination
A/C/E=1-456 P DNA repair
A/C/E=1-456 P histone acetylation
A/C/E=1-456 P histone H2A acetylation
A/C/E=1-456 P histone H4 acetylation
A/C/E=1-456 P positive regulation of canonical Wnt signaling pathway
A/C/E=1-456 P positive regulation of telomerase RNA localization to Cajal body
A/C/E=1-456 P protein deubiquitination
A/C/E=1-456 P regulation of growth
A/C/E=1-456 P regulation of transcription by RNA polymerase II
A/C/E=1-456 P spermatogenesis
B/D/F=1-463 C centrosome
B/D/F=1-463 C cytoplasm
B/D/F=1-463 C cytosol
B/D/F=1-463 C extracellular exosome
B/D/F=1-463 C Ino80 complex
B/D/F=1-463 C intracellular
B/D/F=1-463 C membrane
B/D/F=1-463 C MLL1 complex
B/D/F=1-463 C NuA4 histone acetyltransferase complex
B/D/F=1-463 C nuclear euchromatin
B/D/F=1-463 C nuclear matrix
B/D/F=1-463 C nucleoplasm
B/D/F=1-463 C nucleus
B/D/F=1-463 C R2TP complex
B/D/F=1-463 C ribonucleoprotein complex
B/D/F=1-463 C Swr1 complex
B/D/F=1-463 F 5'-3' DNA helicase activity
B/D/F=1-463 F ADP binding
B/D/F=1-463 F ATP binding
B/D/F=1-463 F ATPase binding
B/D/F=1-463 F beta-catenin binding
B/D/F=1-463 F chromatin DNA binding
B/D/F=1-463 F DNA helicase activity
B/D/F=1-463 F identical protein binding
B/D/F=1-463 F protein homodimerization activity
B/D/F=1-463 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
B/D/F=1-463 F RNA polymerase II core promoter sequence-specific DNA binding
B/D/F=1-463 F TBP-class protein binding
B/D/F=1-463 F TFIID-class transcription factor complex binding
B/D/F=1-463 F transcription corepressor activity
B/D/F=1-463 F unfolded protein binding
B/D/F=1-463 P box C/D snoRNP assembly
B/D/F=1-463 P cellular response to estradiol stimulus
B/D/F=1-463 P cellular response to UV
B/D/F=1-463 P chromatin remodeling
B/D/F=1-463 P DNA recombination
B/D/F=1-463 P DNA repair
B/D/F=1-463 P establishment of protein localization to chromatin
B/D/F=1-463 P histone acetylation
B/D/F=1-463 P histone H2A acetylation
B/D/F=1-463 P histone H4 acetylation
B/D/F=1-463 P negative regulation of canonical Wnt signaling pathway
B/D/F=1-463 P negative regulation of estrogen receptor binding
B/D/F=1-463 P positive regulation of histone acetylation
B/D/F=1-463 P positive regulation of telomerase RNA localization to Cajal body
B/D/F=1-463 P positive regulation of transcription by RNA polymerase II
B/D/F=1-463 P protein folding
B/D/F=1-463 P regulation of growth
B/D/F=1-463 P regulation of transcription by RNA polymerase II
B/D/F=1-463 P transcriptional activation by promoter-enhancer looping
G=267-1556 C cytoplasm
G=267-1556 C Ino80 complex
G=267-1556 C microtubule
G=267-1556 C nuclear body
G=267-1556 C nucleoplasm
G=267-1556 C nucleus
G=267-1556 C plasma membrane
G=267-1556 C spindle
G=267-1556 F actin binding
G=267-1556 F alpha-tubulin binding
G=267-1556 F ATP binding
G=267-1556 F ATPase activity
G=267-1556 F DNA binding
G=267-1556 F DNA-dependent ATPase activity
G=267-1556 F histone binding
G=267-1556 P ATP-dependent chromatin remodeling
G=267-1556 P cell division
G=267-1556 P cellular response to ionizing radiation
G=267-1556 P cellular response to UV
G=267-1556 P chromatin remodeling
G=267-1556 P DNA repair
G=267-1556 P double-strand break repair
G=267-1556 P double-strand break repair via homologous recombination
G=267-1556 P mitotic sister chromatid segregation
G=267-1556 P nucleosome mobilization
G=267-1556 P positive regulation of cell growth
G=267-1556 P positive regulation of nuclear cell cycle DNA replication
G=267-1556 P positive regulation of transcription by RNA polymerase II
G=267-1556 P protein deubiquitination
G=267-1556 P regulation of G1/S transition of mitotic cell cycle
G=267-1556 P regulation of transcription from RNA polymerase II promoter in response to stress
G=267-1556 P spindle assembly
G=267-1556 P transcription, DNA-templated
G=267-1556 P UV-damage excision repair
H=1-607 C cytoplasm
H=1-607 C Ino80 complex
H=1-607 C nucleoplasm
H=1-607 C nucleus
H=1-607 P ATP-dependent chromatin remodeling
H=1-607 P DNA recombination
H=1-607 P double-strand break repair
H=1-607 P protein deubiquitination
H=1-607 P regulation of transcription, DNA-templated
H=1-607 P UV-damage excision repair
I/M=1-136 C extracellular exosome
I/M=1-136 C extracellular region
I/M=1-136 C membrane
I/M=1-136 C nuclear chromosome
I/M=1-136 C nuclear nucleosome
I/M=1-136 C nucleoplasm
I/M=1-136 C nucleosome
I/M=1-136 C nucleus
I/M=1-136 C protein-containing complex
I/M=1-136 F cadherin binding
I/M=1-136 F DNA binding
I/M=1-136 F protein heterodimerization activity
I/M=1-136 P blood coagulation
I/M=1-136 P cellular protein metabolic process
I/M=1-136 P chromatin organization
I/M=1-136 P DNA replication-dependent nucleosome assembly
I/M=1-136 P interleukin-7-mediated signaling pathway
I/M=1-136 P negative regulation of gene expression, epigenetic
I/M=1-136 P nucleosome assembly
I/M=1-136 P rDNA heterochromatin assembly
I/M=1-136 P regulation of gene silencing
I/M=1-136 P regulation of gene silencing by miRNA
I/M=1-136 P regulation of megakaryocyte differentiation
I/M=1-136 P telomere organization
J/N=1-103 C extracellular exosome
J/N=1-103 C extracellular region
J/N=1-103 C host cell nucleus
J/N=1-103 C membrane
J/N=1-103 C nuclear chromosome
J/N=1-103 C nuclear chromosome, telomeric region
J/N=1-103 C nuclear nucleosome
J/N=1-103 C nucleoplasm
J/N=1-103 C nucleosome
J/N=1-103 C nucleus
J/N=1-103 C protein-containing complex
J/N=1-103 F DNA binding
J/N=1-103 F protein domain specific binding
J/N=1-103 F protein heterodimerization activity
J/N=1-103 F RNA binding
J/N=1-103 P cellular protein metabolic process
J/N=1-103 P CENP-A containing nucleosome assembly
J/N=1-103 P DNA replication-dependent nucleosome assembly
J/N=1-103 P DNA replication-independent nucleosome assembly
J/N=1-103 P DNA-templated transcription, initiation
J/N=1-103 P double-strand break repair via nonhomologous end joining
J/N=1-103 P negative regulation of gene expression, epigenetic
J/N=1-103 P negative regulation of megakaryocyte differentiation
J/N=1-103 P nucleosome assembly
J/N=1-103 P rDNA heterochromatin assembly
J/N=1-103 P regulation of gene silencing by miRNA
J/N=1-103 P regulation of megakaryocyte differentiation
J/N=1-103 P telomere capping
J/N=1-103 P telomere organization
K/O=1-130 C extracellular exosome
K/O=1-130 C nuclear chromatin
K/O=1-130 C nucleosome
K/O=1-130 C nucleus
K/O=1-130 F DNA binding
K/O=1-130 F protein heterodimerization activity
K/O=1-130 P chromatin organization
K/O=1-130 P chromatin silencing
K/O=1-130 P negative regulation of cell population proliferation
L/P=1-126 C cytosol
L/P=1-126 C extracellular space
L/P=1-126 C nucleoplasm
L/P=1-126 C nucleosome
L/P=1-126 C nucleus
L/P=1-126 F DNA binding
L/P=1-126 F lipopolysaccharide binding
L/P=1-126 F protein heterodimerization activity
L/P=1-126 P antibacterial humoral response
L/P=1-126 P antimicrobial humoral immune response mediated by antimicrobial peptide
L/P=1-126 P defense response to Gram-negative bacterium
L/P=1-126 P defense response to Gram-positive bacterium
L/P=1-126 P innate immune response in mucosa
L/P=1-126 P killing of cells of other organism
L/P=1-126 P negative regulation of tumor necrosis factor-mediated signaling pathway
L/P=1-126 P nucleosome assembly
L/P=1-126 P protein ubiquitination
R=1-356 C Ino80 complex
R=1-356 C nucleolus
R=1-356 C nucleoplasm
R=1-356 F metal ion binding
R=1-356 P ATP-dependent chromatin remodeling
R=1-356 P DNA recombination
R=1-356 P DNA repair
R=1-356 P protein deubiquitination
Sequences
Download file with secondary structure created by Stride  
6hts.pdb1.pdb:   [ download sequences in FASTA format ]
X (dna): 
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Y (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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I (protein): 
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J (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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R (protein): 
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