4Z2M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.981 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  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

    Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Sakyo-ku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACT complex subunit SPT16
B
287Homo sapiensGene Names: SUPT16H (FACT140, FACTP140)
Find proteins for Q9Y5B9 (Homo sapiens)
Go to Gene View: SUPT16H
Go to UniProtKB:  Q9Y5B9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
G, I
102Homo sapiensGene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
H, J
103Homo sapiensGene 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.981 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 65.442α = 90.00
b = 69.784β = 90.00
c = 187.853γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Database references