5BO0

Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer

• PDB DOI:  https://doi.org/10.2210/pdb5BO0/pdb

• Classification: CHAPERONE/DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

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

• PubMed: 26167883 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.36 kDa 
• Atom Count: 2,970 
• Modelled Residue Count: 374 
• Deposited Residue Count: 410 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A	80	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D, H3C15, H3C14, H3C13
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	102	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	C	70	Homo sapiens	Mutation(s): 0  Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens) Explore P49736  Go to UniProtKB:  P49736
PHAROS:  P49736

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone chaperone ASF1B	D	158	Homo sapiens	Mutation(s): 0  Gene Names: ASF1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVP2 (Homo sapiens) Explore Q9NVP2  Go to UniProtKB:  Q9NVP2
PHAROS:  Q9NVP2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.964	α = 90
b = 112.964	β = 90
c = 98.226	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• 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