7CJ0

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

  • Classification: CHAPERONE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2020-07-09 Released: 2021-04-14 
  • Deposition Author(s): Bao, H., Huang, H.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3A [auth E],
E [auth B]
79Homo sapiensMutation(s): 0 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
Entity Groups  
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UniProt GroupP84243
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4B [auth F],
F [auth C]
102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2C [auth G],
G [auth H]
70Homo sapiensMutation(s): 0 
Gene Names: MCM2
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens)
Explore P49736 
Go to UniProtKB:  P49736
PHAROS:  P49736
GTEx:  ENSG00000073111 
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UniProt GroupP49736
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ homolog subfamily C member 9D,
H [auth A]
84Homo sapiensMutation(s): 1 
Gene Names: DNAJC9
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WXX5 (Homo sapiens)
Explore Q8WXX5 
Go to UniProtKB:  Q8WXX5
GTEx:  ENSG00000213551 
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UniProt GroupQ8WXX5
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.51α = 90
b = 47.51β = 90
c = 616.26γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description