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- EMDB-71627: Human SRCAP-nucleosome complex in the fully-engaged state, with H... -

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Basic information

Entry
Database: EMDB / ID: EMD-71627
TitleHuman SRCAP-nucleosome complex in the fully-engaged state, with H4-bound GAS41 (unmasked refinement, filtered by local resolution)
Map data
Sample
  • Complex: SRCAP-nucleosome complex
KeywordsChromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION
Function / homology
Function and homology information


positive regulation of lymphoid progenitor cell differentiation / histone H3K18ac reader activity / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / npBAF complex / RPAP3/R2TP/prefoldin-like complex / brahma complex / positive regulation of norepinephrine uptake ...positive regulation of lymphoid progenitor cell differentiation / histone H3K18ac reader activity / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / npBAF complex / RPAP3/R2TP/prefoldin-like complex / brahma complex / positive regulation of norepinephrine uptake / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / GBAF complex / histone chaperone activity / R2TP complex / dynein axonemal particle / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / RSC-type complex / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Swr1 complex / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / heart process / establishment of protein localization to chromatin / regulation of G0 to G1 transition / dense body / Tat protein binding / Folding of actin by CCT/TriC / Regulation of CDH1 Function / Ino80 complex / postsynaptic actin cytoskeleton / negative regulation of transcription by RNA polymerase I / apical protein localization / Adherens junctions interactions / Prefoldin mediated transfer of substrate to CCT/TriC / microtubule nucleation / RHOF GTPase cycle / adherens junction assembly / regulation of double-strand break repair / box C/D snoRNP assembly / SWI/SNF complex / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / spinal cord development / tight junction / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / nucleolus organization / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / regulation of chromosome organization / histone H3K27ac reader activity / regulation of norepinephrine uptake / Recycling pathway of L1 / transporter regulator activity / positive regulation of double-strand break repair / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / establishment or maintenance of cell polarity / negative regulation of cell differentiation / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / TFIID-class transcription factor complex binding / regulation of DNA replication / positive regulation of DNA damage response, signal transduction by p53 class mediator / : / MLL1 complex / brush border / EPH-ephrin mediated repulsion of cells / positive regulation of transcription initiation by RNA polymerase II / Telomere Extension By Telomerase / protein folding chaperone complex / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / calcium ion homeostasis / cAMP/PKA signal transduction / kinesin binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane
Similarity search - Function
DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Vps71/ZNHIT1 / YEATS / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal ...DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Vps71/ZNHIT1 / YEATS / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / : / YEATS superfamily / YEATS family / YEATS domain profile. / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / domain in helicases and associated with SANT domains / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Zinc finger HIT domain-containing protein 1 / YEATS domain-containing protein 4 / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Actin, cytoplasmic 1 / Histone H4 / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP ...Zinc finger HIT domain-containing protein 1 / YEATS domain-containing protein 4 / Actin-like protein 6A / Histone H2B 1.1 / Histone H2A type 1 / Actin, cytoplasmic 1 / Histone H4 / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP / Actin-related protein 6 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 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
DepositionJul 7, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71627.png

Downloads & links

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Map

FileDownload / File: emd_71627.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
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.019860841 - 0.056204
Average (Standard dev.)-0.000015520334 (±0.0026345814)
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_71627_msk_1.map
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Half map: #1

Fileemd_71627_half_map_1.map
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Half map: #2

Fileemd_71627_half_map_2.map
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Sample components

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Entire : SRCAP-nucleosome complex

EntireName: SRCAP-nucleosome complex
Components
  • Complex: SRCAP-nucleosome complex

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Supramolecule #1: SRCAP-nucleosome complex

SupramoleculeName: SRCAP-nucleosome complex / type: complex / ID: 1 / Parent: 0
Details: Endogenous purified SRCAP bound to 106N32 nucleosome
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 / Details: Negative stain reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 5605
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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