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- EMDB-71626: ARP6-ZNHIT1 module from fully-engaged state of SRCAP-nucleosome c... -

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Basic information

Entry
Database: EMDB / ID: EMD-71626
TitleARP6-ZNHIT1 module from fully-engaged state of SRCAP-nucleosome complex, with H3-bound ARP6 (focused refinement, filtered by local resolution)
Map data
Sample
  • Complex: SRCAP-nucleosome complex
    • Protein or peptide: Actin-related protein 6
    • Protein or peptide: Zinc finger HIT domain-containing protein 1
    • Protein or peptide: Histone H3.2
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsChromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION
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 / histone binding / structural constituent of chromatin / nucleosome / heterochromatin formation / cytoskeleton / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / 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
Zinc finger HIT domain-containing protein 1 / Histone H3.2 / Actin-related protein 6
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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_71626.png

Downloads & links

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Map

FileDownload / File: emd_71626.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 0.025
Minimum - Maximum-0.090431 - 0.19669084
Average (Standard dev.)0.000023344459 (±0.0013927339)
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_71626_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_71626_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71626_half_map_2.map
Projections & Slices
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Sample components

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Entire : SRCAP-nucleosome complex

EntireName: SRCAP-nucleosome complex
Components
  • Complex: SRCAP-nucleosome complex
    • Protein or peptide: Actin-related protein 6
    • Protein or peptide: Zinc finger HIT domain-containing protein 1
    • Protein or peptide: Histone H3.2
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: SRCAP-nucleosome complex

SupramoleculeName: SRCAP-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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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Macromolecule #1: Actin-related protein 6

MacromoleculeName: Actin-related protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 45.857902 KDa
SequenceString: MTTLVLDNGA YNAKIGYSHE NVSVIPNCQF RSKTARLKTF TANQIDEIKD PSGLFYILPF QKGYLVNWDV QRQVWDYLFG KEMYQVDFL DTNIIITEPY FNFTSIQESM NEILFEEYQF QAVLRVNAGA LSAHRYFRDN PSELCCIIVD SGYSFTHIVP Y CRSKKKKE ...String:
MTTLVLDNGA YNAKIGYSHE NVSVIPNCQF RSKTARLKTF TANQIDEIKD PSGLFYILPF QKGYLVNWDV QRQVWDYLFG KEMYQVDFL DTNIIITEPY FNFTSIQESM NEILFEEYQF QAVLRVNAGA LSAHRYFRDN PSELCCIIVD SGYSFTHIVP Y CRSKKKKE AIIRINVGGK LLTNHLKEII SYRQLHVMDE THVINQVKED VCYVSQDFYR DMDIAKLKGE ENTVMIDYVL PD FSTIKKG FCKPREEMVL SGKYKSGEQI LRLANERFAV PEILFNPSDI GIQEMGIPEA IVYSIQNLPE EMQPHFFKNI VLT GGNSLF PGFRDRVYSE VRCLTPTDYD VSVVLPENPI TYAWEGGKLI SENDDFEDMV VTREDYEENG HSVCEEKFDI

UniProtKB: Actin-related protein 6

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Macromolecule #2: Zinc finger HIT domain-containing protein 1

MacromoleculeName: Zinc finger HIT domain-containing protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 17.567023 KDa
SequenceString:
MVEKKTSVRS QDPGQRRVLD RAARQRRINR QLEALENDNF QDDPHAGLPQ LGKRLPQFDD DADTGKKKKK TRGDHFKLRF RKNFQALLE EQNLSVAEGP NYLTACAGPP SRPQRPFCAV CGFPSPYTCV SCGARYCTVR CLGTHQETRC LKWTV

UniProtKB: Zinc finger HIT domain-containing protein 1

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 227030
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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