6HTS

Cryo-EM structure of the human INO80 complex bound to nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and regulation of the human INO80-nucleosome complex.

Ayala, R.Willhoft, O.Aramayo, R.J.Wilkinson, M.McCormack, E.A.Ocloo, L.Wigley, D.B.Zhang, X.

(2018) Nature 556: 391-395


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RuvB-like 1
A, C, E
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1 (INO80H, NMP238, TIP49, TIP49A)
EC: 3.6.4.12
Find proteins for Q9Y265 (Homo sapiens)
Go to Gene View: RUVBL1
Go to UniProtKB:  Q9Y265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RuvB-like 2
B, D, F
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2 (INO80J, TIP48, TIP49B)
EC: 3.6.4.12
Find proteins for Q9Y230 (Homo sapiens)
Go to Gene View: RUVBL2
Go to UniProtKB:  Q9Y230
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chromatin-remodeling ATPase INO80
G
1290Homo sapiensMutation(s): 0 
Gene Names: INO80 (INO80A, INOC1, KIAA1259)
EC: 3.6.4.-
Find proteins for Q9ULG1 (Homo sapiens)
Go to Gene View: INO80
Go to UniProtKB:  Q9ULG1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 5
H
607Homo sapiensMutation(s): 0 
Gene Names: ACTR5 (ARP5)
Find proteins for Q9H9F9 (Homo sapiens)
Go to Gene View: ACTR5
Go to UniProtKB:  Q9H9F9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
I, M
136Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H4
J, N
103Homo 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 UniProtKB:  P62805
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
K, O
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens)
Go to Gene View: HIST1H2AB HIST1H2AE
Go to UniProtKB:  P04908
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
L, P
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
INO80 complex subunit B
R
356Homo sapiensMutation(s): 0 
Gene Names: INO80B (HMGA1L4, PAPA1, ZNHIT4)
Find proteins for Q9C086 (Homo sapiens)
Go to Gene View: INO80B
Go to UniProtKB:  Q9C086
Entity ID: 10
MoleculeChainsLengthOrganism
DNA (150-MER)X228synthetic construct
Entity ID: 11
MoleculeChainsLengthOrganism
DNA (150-MER)Y228synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098412/Z/12/Z
Wellcome TrustUnited Kingdom095519/Z/11/Z
Cancer Research UKUnited KingdomC6913/A21608

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release