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- PDB-9pgc: Trident submodule from human SRCAP-nucleosome complex in the full... -

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Basic information

Entry
Database: PDB / ID: 9pgc
TitleTrident submodule from human SRCAP-nucleosome complex in the fully-engaged state (focused refinement)
Components
  • (DNA) x 2
  • Actin-like protein 6A
  • Helicase SRCAP
  • Vacuolar protein sorting-associated protein 72 homolog
KeywordsGENE REGULATION / Chromatin Remodeler / Snf2 family ATPase / H2A.Z
Function / homology
Function and homology information


npBAF complex / brahma complex / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / GBAF complex / histone chaperone activity / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the canonical BAF (cBAF) complex / RSC-type complex ...npBAF complex / brahma complex / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / GBAF complex / histone chaperone activity / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the canonical BAF (cBAF) complex / RSC-type complex / Formation of the polybromo-BAF (pBAF) complex / Swr1 complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / regulation of G0 to G1 transition / Ino80 complex / regulation of double-strand break repair / SWI/SNF complex / ATP-dependent chromatin remodeler activity / spinal cord development / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of chromosome organization / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / positive regulation of myoblast differentiation / cAMP/PKA signal transduction / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / telomere maintenance / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / kinetochore / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / RMTs methylate histone arginines / nervous system development / nucleosome / UCH proteinases / histone binding / HATs acetylate histones / regulation of cell cycle / nuclear body / regulation of apoptotic process / transcription coactivator activity / nuclear speck / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / signal transduction / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
Vps72/YL1, N-terminal / YL1 nuclear protein / : / 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 / HSA domain ...Vps72/YL1, N-terminal / YL1 nuclear protein / : / 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 / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin, conserved site / Actins signature 2. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA (> 100) / Actin-like protein 6A / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLouder, R.K. / Park, G.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase SRCAP
B: Vacuolar protein sorting-associated protein 72 homolog
K: Actin-like protein 6A
Y: DNA
Z: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)609,2219
Polymers608,1265
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ABK

#1: Protein Helicase SRCAP / Domino homolog 2 / Snf2-related CBP activator


Mass: 343915.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW
References: UniProt: Q6ZRS2, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Vacuolar protein sorting-associated protein 72 homolog / Protein YL-1 / Transcription factor-like 1


Mass: 40658.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: Q15906
#3: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: K-562 / Organ: BLOOD / Tissue: BONE MARROW / References: UniProt: O96019

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DNA chain , 2 types, 2 molecules YZ

#4: DNA chain DNA


Mass: 87851.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA


Mass: 88190.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1SRCAP-nucleosome complexCOMPLEXEndogenous purified SRCAP bound to 106N32 nucleosome#1-#50MULTIPLE SOURCES
2Endogenous human SRCAP complexCOMPLEX#1-#31NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: K-562 / Cellular location: NUCLEOPLASM / Organ: BLOOD / Organelle: NUCLEUS / Tissue: BONE MARROW
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21_5207model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57610 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 120 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00399418
ELECTRON MICROSCOPYf_angle_d0.56412823
ELECTRON MICROSCOPYf_chiral_restr0.0411411
ELECTRON MICROSCOPYf_plane_restr0.00661546
ELECTRON MICROSCOPYf_dihedral_angle_d16.6941481

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