5BNV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.795 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
A, D
79Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, E
102Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM2
F, C
70Homo sapiensMutation(s): 0 
Gene Names: MCM2 (BM28, CCNL1, CDCL1, KIAA0030)
EC: 3.6.4.12
Find proteins for P49736 (Homo sapiens)
Go to Gene View: MCM2
Go to UniProtKB:  P49736
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.795 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.592α = 90.00
b = 110.592β = 90.00
c = 203.265γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2015-07-29
    Type: Database references
  • Version 1.3: 2015-08-19
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description