9ZLA | pdb_00009zla

Unbound 106-N-32 nucleosome from SRCAP-CFDP1-nucleosome binding reaction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme.

Park, G.Wu, C.Louder, R.K.

(2026) Sci Adv 12: eaei7728-eaei7728

  • DOI: https://doi.org/10.1126/sciadv.aei7728
  • Primary Citation Related Structures: 
    9CA7, 9CA8, 9CA9, 9CAA, 9NFV, 9NFW, 9NFX, 9NFY, 9NFZ, 9NG0, 9PGC, 9PGD, 9Y3D, 9Y3E, 9Y3F, 9Y3G, 9Y3H, 9ZLA

  • PubMed Abstract: 

    The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that histone exchange by SRCAP requires the transient activator CFDP1 and resolve nine cryo-electron microscopy structures of the SRCAP-CFDP1 holoenzyme that define the stepwise exchange mechanism. CFDP1 recognizes the conformation of the fully engaged SRCAP-nucleosome complex through interactions with multiple subunits-including direct contact with the ATPase domain-and induces conformational transitions that drive extensive DNA unwrapping, eviction of the H2A-H2B dimer, and insertion of the H2A.Z-H2B dimer, all without necessarily requiring hydrolysis of bound ATP. Collectively, these findings provide unprecedented insight into the mechanism of activator- and nucleotide-driven histone exchange from nucleosomal H2A to H2A.Z.


  • Organizational Affiliation
    • Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Macromolecule Content 

  • Total Structure Weight: 284.69 kDa 
  • Atom Count: 12,443 
  • Modeled Residue Count: 1,080 
  • Deposited Residue Count: 1,550 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1A [auth Q],
C [auth S]
128Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
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UniProt GroupP06897
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B 1.1B [auth R],
D [auth T]
125Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.2E [auth U],
G [auth W]
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
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UniProt GroupP84233
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4F [auth V],
H [auth X]
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
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UniProt GroupP62799
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (285-MER)I [auth Y]285synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (285-MER)J [auth Z]285synthetic construct
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release