6FML

CryoEM Structure INO80core Nucleosome complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.

Eustermann, S., Schall, K., Kostrewa, D., Lakomek, K., Strauss, M., Moldt, M., Hopfner, K.P.

(2018) Nature 556: 386-390


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RuvB-like helicase
A, B, C
462Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
EC: 3.6.4.12
Find proteins for G0RYI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYI5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RuvB-like helicase
D, E, F
488Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
EC: 3.6.4.12
Find proteins for G0RYC2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYC2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ino80
G
1856N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
les2
H
491Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY01 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY01
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ies6
I
219Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S590 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S590
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin related protein 5
J
770Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S589 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S589
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
M, Q
135Homo sapiensMutation(s): 0 
Gene Names: HIST2H3A, HIST2H3C, HIST2H3D (H3F2, H3FM)
Find proteins for Q71DI3 (Homo sapiens)
Go to Gene View: HIST2H3A HIST2H3C HIST2H3D
Go to UniProtKB:  Q71DI3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Histone H4
N, R
102Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4
Go to UniProtKB:  P62805
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
O, S
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM (H2AFP, H2AFC, H2AFD, H2AFI, H2AFN)
Find proteins for P0C0S8 (Homo sapiens)
Go to Gene View: HIST1H2AG HIST1H2AI HIST1H2AK HIST1H2AL HIST1H2AM
Go to UniProtKB:  P0C0S8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-C/E/F/G/I
P, T
125Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI (H2BFL, H2BFH, H2BFG, H2BFA, H2BFK)
Find proteins for P62807 (Homo sapiens)
Go to Gene View: HIST1H2BC HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BI
Go to UniProtKB:  P62807
Entity ID: 7
MoleculeChainsLengthOrganism
Nucleosomal DNA Strand 1K196synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
Nucleosomal DNA Strand 2L196synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
J
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
H, J
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyEMBO ALTF 1098-2012
European Research CouncilGermanyATMMACHINE
German Research FoundationGermanyCRC1064, GRK1721

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references