7CIZ

Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network.

Hammond, C.M.Bao, H.Hendriks, I.A.Carraro, M.Garcia-Nieto, A.Liu, Y.Reveron-Gomez, N.Spanos, C.Chen, L.Rappsilber, J.Nielsen, M.L.Patel, D.J.Huang, H.Groth, A.

(2021) Mol Cell 81: 2533-2548.e9

  • DOI: 10.1016/j.molcel.2021.03.041
  • Primary Citation of Related Structures:  
    7CIZ, 7CJ0

  • PubMed Abstract: 
  • From biosynthesis to assembly into nucleosomes, histones are handed through a cascade of histone chaperones, which shield histones from non-specific interactions. Whether mechanisms exist to safeguard the histone fold during histone chaperone handover events or to release trapped intermediates is unclear ...

    From biosynthesis to assembly into nucleosomes, histones are handed through a cascade of histone chaperones, which shield histones from non-specific interactions. Whether mechanisms exist to safeguard the histone fold during histone chaperone handover events or to release trapped intermediates is unclear. Using structure-guided and functional proteomics, we identify and characterize a histone chaperone function of DNAJC9, a heat shock co-chaperone that promotes HSP70-mediated catalysis. We elucidate the structure of DNAJC9, in a histone H3-H4 co-chaperone complex with MCM2, revealing how this dual histone and heat shock co-chaperone binds histone substrates. We show that DNAJC9 recruits HSP70-type enzymes via its J domain to fold histone H3-H4 substrates: upstream in the histone supply chain, during replication- and transcription-coupled nucleosome assembly, and to clean up spurious interactions. With its dual functionality, DNAJC9 integrates ATP-resourced protein folding into the histone supply pathway to resolve aberrant intermediates throughout the dynamic lives of histones.


    Organizational Affiliation

    Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark. Electronic address: anja.groth@cpr.ku.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3A,
D [auth E],
G [auth I]
79Homo sapiensMutation(s): 0 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
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PHAROS:  P84243
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UniProt GroupP84243
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B,
E [auth F],
H [auth J]
102Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2C,
F [auth G],
I [auth K]
70Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
EC: 3.6.4.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DnaJ homolog subfamily C member 9J [auth D],
K [auth H],
L
75Homo sapiensMutation(s): 1 
Gene Names: DNAJC9
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UniProt GroupQ8WXX5
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.638α = 90
b = 176.816β = 90
c = 202.925γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-07-08 
  • Released Date: 2021-04-14 
  • Deposition Author(s): Bao, H., Huang, H.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFC1004500
National Natural Science Foundation of China (NSFC)Chinathe Thousand Young Talents Program
National Natural Science Foundation of China (NSFC)China31800619

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references