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- EMDB-74337: Prenucleosome from pre-inserted state of SRCAP-CFDP1-prenucleosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-74337
TitlePrenucleosome from pre-inserted state of SRCAP-CFDP1-prenucleosome complex, subclass with alternative dimer position B (focused refinement)
Map data
Sample
  • Complex: SRCAP-CFDP1-prenucleosome complex
    • Complex: Endogenous human SRCAP complex
KeywordsChromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsLouder RK / Park G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme.
Authors: Giho Park / Carl Wu / Robert K Louder /
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 ...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.
History
DepositionDec 5, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74337.png

Downloads & links

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Map

FileDownload / File: emd_74337.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 393.6 Å		1.03 Å/pix.
x 384 pix.
= 393.6 Å		1.03 Å/pix.
x 384 pix.
= 393.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04250646 - 0.061071165
Average (Standard dev.)0.000036294245 (±0.0010375036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74337_msk_1.map
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Additional map: Map filtered by local resolution

Fileemd_74337_additional_1.map
AnnotationMap filtered by local resolution
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Additional map: Map postprocessed with DeepEMhancer

Fileemd_74337_additional_2.map
AnnotationMap postprocessed with DeepEMhancer
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Half map: #1

Fileemd_74337_half_map_1.map
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Half map: #2

Fileemd_74337_half_map_2.map
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Sample components

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Entire : SRCAP-CFDP1-prenucleosome complex

EntireName: SRCAP-CFDP1-prenucleosome complex
Components
  • Complex: SRCAP-CFDP1-prenucleosome complex
    • Complex: Endogenous human SRCAP complex

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Supramolecule #1: SRCAP-CFDP1-prenucleosome complex

SupramoleculeName: SRCAP-CFDP1-prenucleosome complex / type: complex / ID: 1 / Parent: 0
Details: Endogenous purified SRCAP bound to CFDP1 and 106N32 prenucleosome
Source (natural)Organism: Homo sapiens (human) / Strain: K-562 / Organ: BLOOD / Tissue: BONE MARROW / Organelle: NUCLEUS / Location in cell: NUCLEOPLASM

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Supramolecule #2: Endogenous human SRCAP complex

SupramoleculeName: Endogenous human SRCAP complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Strain: K-562 / Organ: BLOOD / Tissue: BONE MARROW / Organelle: NUCLEUS / Location in cell: NUCLEOPLASM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 2482
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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