6FTX

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.

Sundaramoorthy, R.Hughes, A.L.El-Mkami, H.Norman, D.G.Ferreira, H.Owen-Hughes, T.

(2018) Elife 7: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A
97Petromyzon marinusMutation(s): 0 
Find proteins for S4RAZ3 (Petromyzon marinus)
Go to UniProtKB:  S4RAZ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
126Xenopus tropicalisMutation(s): 0 
Gene Names: hist2h2bf (LOC100495396)
Find proteins for Q28D68 (Xenopus tropicalis)
Go to UniProtKB:  Q28D68
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3C
E
110Xenopus laevisMutation(s): 0 
Gene Names: h3f3c
Find proteins for P02302 (Xenopus laevis)
Go to UniProtKB:  P02302
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
N, O
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Chromatin-remodeling ATPase
W
878Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.-
Find proteins for P32657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CHD1
Go to UniProtKB:  P32657
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (159-MER)I159synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (160-MER)J160synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
W
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
W
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Refinement description, Structure summary