5BNV

Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks.

Huang, H.Strmme, C.B.Saredi, G.Hodl, M.Strandsby, A.Gonzalez-Aguilera, C.Chen, S.Groth, A.Patel, D.J.

(2015) Nat Struct Mol Biol 22: 618-626

  • DOI: https://doi.org/10.1038/nsmb.3055
  • Primary Citation of Related Structures:  
    5BNV, 5BNX, 5BO0

  • PubMed Abstract: 

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase, chaperones histones H3-H4. Our first structure shows an H3-H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. Our second structure reveals MCM2 and ASF1 cochaperoning an H3-H4 dimer. Mutational analyses show that the MCM2 HBD is required for MCM2-7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3-H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling histones genome wide during DNA replication.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3A,
C [auth D]
79Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
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Go to UniProtKB:  P84243
PHAROS:  P84243
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UniProt GroupP84243
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4B,
D [auth E]
102Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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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 MCM2E [auth F],
F [auth C]
70Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.592α = 90
b = 110.592β = 90
c = 203.265γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2015-07-29
    Changes: Database references
  • Version 1.3: 2015-08-19
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.5: 2021-03-10
    Changes: Data collection
  • Version 1.6: 2024-03-06
    Changes: Data collection, Database references