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- PDB-9pgd: ARP6-ZNHIT1 module from fully-engaged state of SRCAP-nucleosome c... -

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Basic information

Entry
Database: PDB / ID: 9pgd
TitleARP6-ZNHIT1 module from fully-engaged state of SRCAP-nucleosome complex, with H3-bound ARP6 (focused refinement, filtered by local resolution)
Components
  • Actin-related protein 6
  • Histone H3.2
  • Zinc finger HIT domain-containing protein 1
KeywordsGENE REGULATION / Chromatin Remodeler / Snf2 family ATPase / H2A.Z
Function / homology
Function and homology information


positive regulation of lymphoid progenitor cell differentiation / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / muscle cell differentiation / Swr1 complex / heart process / negative regulation of transcription by RNA polymerase I / nucleolus organization / positive regulation of transcription by RNA polymerase I / positive regulation of DNA damage response, signal transduction by p53 class mediator ...positive regulation of lymphoid progenitor cell differentiation / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / muscle cell differentiation / Swr1 complex / heart process / negative regulation of transcription by RNA polymerase I / nucleolus organization / positive regulation of transcription by RNA polymerase I / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of transcription initiation by RNA polymerase II / calcium ion homeostasis / nucleosome binding / transcription initiation-coupled chromatin remodeling / histone deacetylase binding / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / histone binding / heterochromatin formation / cytoskeleton / chromatin remodeling / protein heterodimerization activity / nucleolus / regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Histone H3 signature 1. / Histone H3 signature 2. ...Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Actin / Actin family / Actin / 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
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Zinc finger HIT domain-containing protein 1 / Histone H3.2 / Actin-related protein 6
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
C: Actin-related protein 6
D: Zinc finger HIT domain-containing protein 1
U: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4077
Polymers78,7293
Non-polymers6784
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 CDU

#1: Protein Actin-related protein 6 / hArp6 / hARPX


Mass: 45857.902 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: Q9GZN1
#2: Protein Zinc finger HIT domain-containing protein 1 / Cyclin-G1-binding protein 1 / Zinc finger protein subfamily 4A member 1 / p18 Hamlet


Mass: 17567.023 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: O43257
#3: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233

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Non-polymers , 3 types, 4 molecules

#4: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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

ComponentName: SRCAP-nucleosome complex / Type: COMPLEX
Details: Endogenous purified SRCAP bound to 106N32 nucleosome
Entity ID: #1-#3 / Source: MULTIPLE SOURCES
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227030 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00574345
ELECTRON MICROSCOPYf_angle_d0.59555887
ELECTRON MICROSCOPYf_chiral_restr0.0469632
ELECTRON MICROSCOPYf_plane_restr0.0065769
ELECTRON MICROSCOPYf_dihedral_angle_d8.9416597

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