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

Basic information

Entry

Database: EMDB / ID: EMD-71627

• Title: Human SRCAP-nucleosome complex in the fully-engaged state, with H4-bound GAS41 (unmasked refinement, filtered by local resolution)

Sample

• Complex: SRCAP-nucleosome complex

• Keywords: Chromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION

Function / homology

Function:

positive regulation of lymphoid progenitor cell differentiation / histone H3K18ac reader activity / catalytic activity, acting on a protein / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / npBAF complex / positive regulation of norepinephrine uptake / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / 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 / regulation of transepithelial transport / Activation of the TFAP2 (AP-2) family of transcription factors / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Swr1 complex / Formation of the polybromo-BAF (pBAF) complex / Gap junction degradation / GBP-mediated host defense / protein localization to adherens junction / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / establishment of protein localization to chromatin / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / heart process / regulation of G0 to G1 transition / dense body / Folding of actin by CCT/TriC / Tat protein binding / postsynaptic actin cytoskeleton / Ino80 complex / Regulation of CDH1 Function / apical protein localization / negative regulation of transcription by RNA polymerase I / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / regulation of double-strand break repair / microtubule nucleation / SWI/SNF complex / adherens junction assembly / RHOF GTPase cycle / box C/D snoRNP assembly / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / tight junction / Sensory processing of sound by inner hair cells of the cochlea / nucleolus organization / regulation of mitotic metaphase/anaphase transition / positive regulation of DNA damage response, signal transduction by p53 class mediator / spinal cord development / positive regulation of T cell differentiation / 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 / regulation of chromosome organization / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / histone H3K27ac reader activity / Recycling pathway of L1 / cortical cytoskeleton / positive regulation of double-strand break repair / MLL1 complex / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / establishment or maintenance of cell polarity / regulation of DNA replication / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / TFIID-class transcription factor complex binding / brush border / EPH-ephrin mediated repulsion of cells / protein folding chaperone complex / Telomere Extension By Telomerase / positive regulation of transcription initiation by RNA polymerase II / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / cAMP/PKA signal transduction / kinesin binding / RNA polymerase II core promoter sequence-specific DNA binding / calcium ion homeostasis / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / nucleosome binding

Domain/homology:

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 / YEATS / Vps71/ZNHIT1 / 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 / 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 / domain in helicases and associated with SANT domains / 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 / Histone H3 signature 1. / ATPase, nucleotide binding domain / 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

Component:

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

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 7.1 Å
• Authors: Louder RK / Park G

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		United States

• Citation: Journal: 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 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

Deposition	Jul 7, 2025	-
Header (metadata) release	Jul 22, 2026	-
Map release	Jul 22, 2026	-
Update	Aug 12, 2026	-
Current status	Aug 12, 2026	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_71627.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.025 Å

Density

Contour Level	By AUTHOR: 0.0065
Minimum - Maximum	-0.019860841 - 0.056204
Average (Standard dev.)	-0.000015520334 (±0.0026345814)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 393.59998 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_71627_msk_1.map

Half map: #1

• File: emd_71627_half_map_1.map

Half map: #2

• File: emd_71627_half_map_2.map

Sample components

Entire : SRCAP-nucleosome complex

• Entire: Name: SRCAP-nucleosome complex

Components

• Complex: SRCAP-nucleosome complex

Supramolecule #1: SRCAP-nucleosome complex

• Supramolecule: Name: 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

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.6
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination 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

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER / Details: Negative stain reconstruction
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 5605
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD