6UPL

Structure of FACT_subnucleosome complex 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

FACT caught in the act of manipulating the nucleosome.

Liu, Y.Zhou, K.Zhang, N.Wei, H.Tan, Y.Z.Zhang, Z.Carragher, B.Potter, C.S.D'Arcy, S.Luger, K.

(2020) Nature 577: 426-431

  • DOI: 10.1038/s41586-019-1820-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone 'FAcilitates Chromatin Transcription' (FACT; consisting of subunits SPT16 and SSRP1 <sup>1 </sup>) promotes both disass ...

    The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone 'FAcilitates Chromatin Transcription' (FACT; consisting of subunits SPT16 and SSRP1 1 ) promotes both disassembly and reassembly of nucleosomes during gene transcription, DNA replication, and repair 2 . The mechanism by which FACT causes these opposing outcomes is unknown. Here we report two cryo-EM structures of human FACT in complex with partially assembled sub-nucleosomes, with supporting biochemical and hydrogen-deuterium exchange (HDX) data. FACT is engaged in extensive interactions with nucleosomal DNA and all histones. The large DNA-binding surface on FACT appears to be protected by the C-terminal domains of both subunits, and this inhibition is released by interaction with H2A-H2B, allowing FACT-H2A-H2B to dock onto a (H3-H4) 2 -DNA complex 3 . SPT16 binds nucleosomal DNA and tethers H2A-H2B through its C-terminal domain by acting as a placeholder for DNA. SSRP1 also contributes to DNA binding, and can assume two conformations, depending on whether a second H2A-H2B dimer is present. Our data suggest a compelling mechanism for how FACT maintains chromatin integrity during polymerase passage, by facilitating H2A-H2B dimer removal, stabilizing intermediate 'sub-nucleosomal' states, and promoting nucleosome reassembly. Our findings reconcile discrepancies regarding the many roles of FACT and underscore the dynamic interactions between histone chaperones and nucleosomes.


    Organizational Affiliation

    Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA. karolin.luger@colorado.edu.,Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA. karolin.luger@colorado.edu.,The University of Texas at Dallas, Department of Chemistry and Biochemistry, Dallas, TX, USA.,Biochemistry and Molecular Biophysics Dept., Columbia University Medical Center, New York, NY, USA.,National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
136Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, K
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AC (H2AFL)
Find proteins for Q93077 (Homo sapiens)
Go to Gene View: HIST1H2AC
Go to UniProtKB:  Q93077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, L
126Homo sapiensMutation(s): 0 
Gene Names: H2BC4, H2BC6, H2BC7, H2BC8, H2BC10 (H2BFL, HIST1H2BC, H2BFH, HIST1H2BE, H2BFG, HIST1H2BF, H2BFA, HIST1H2BG, H2BFK, HIST1H2BI)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
FACT complex subunit SPT16
G
966N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
FACT complex subunit SSRP1
H
640N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (79-mer)I79Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
DNA (79-mer)J79Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G, H
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Author supporting evidence
  • Version 1.2: 2020-01-29
    Type: Database references