4Z2M

Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Integrated molecular mechanism directing nucleosome reorganization by human FACT.

Tsunaka, Y.Fujiwara, Y.Oyama, T.Hirose, S.Morikawa, K.

(2016) Genes Dev 30: 673-686

  • DOI: 10.1101/gad.274183.115
  • Primary Citation of Related Structures:  
    4Z2M, 4Z2N

  • PubMed Abstract: 
  • Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome ...

    Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone.


    Organizational Affiliation

    Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan; International Institute for Advanced Studies, Kizugawa-shi, Kyoto 619-0225, Japan;



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACT complex subunit SPT16B287Homo sapiensMutation(s): 0 
Gene Names: SUPT16HFACT140FACTP140
Find proteins for Q9Y5B9 (Homo sapiens)
Explore Q9Y5B9 
Go to UniProtKB:  Q9Y5B9
NIH Common Fund Data Resources
PHAROS  Q9Y5B9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1GI102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4HJ103Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.442α = 90
b = 69.784β = 90
c = 187.853γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2016-03-30
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations