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 1.4 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: 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3AD79Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BE102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2CF70Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
EC: 3.6.4.12
Find proteins for P49736 (Homo sapiens)
Explore P49736 
Go to UniProtKB:  P49736
NIH Common Fund Data Resources
PHAROS  P49736
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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

  • Deposited Date: 2015-05-26 
  • Released Date: 2015-06-17 
  • Deposition Author(s): Huang, H., Patel, D.J.

Revision History 

  • 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