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

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Open data


ID or keywords:

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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 DNA damage response, signal transduction by p53 class mediator / positive regulation of transcription by RNA polymerase I ...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 DNA damage response, signal transduction by p53 class mediator / positive regulation of transcription by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / calcium ion homeostasis / nucleosome binding / transcription initiation-coupled chromatin remodeling / histone deacetylase binding / structural constituent of chromatin / nucleosome / histone binding / cytoskeleton / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / DNA-templated transcription / DNA binding / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Actin / Actin family / Actin / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. ...Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Actin / Actin family / Actin / 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
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: To Be Published
Title: Human CFDP1 activates SRCAP complex to catalyze histone H2A.Z exchange
Authors: Park G / Wu C / Louder RK
History
DepositionJul 7, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71626_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71626_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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