[English] 日本語
Yorodumi
- EMDB-74396: Unbound 106-N-32 nucleosome from SRCAP-CFDP1-nucleosome binding r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74396
TitleUnbound 106-N-32 nucleosome from SRCAP-CFDP1-nucleosome binding reaction
Map data
Sample
  • Complex: 106N32 nucleosome
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: DNA (285-MER)
    • DNA: DNA (285-MER)
KeywordsChromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION
Function / homology
Function and homology information


nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / chromatin organization / protein heterodimerization activity ...nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / chromatin organization / protein heterodimerization activity / DNA binding / : / nucleoplasm / nucleus
Similarity search - Function
: / 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 ...: / 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 / 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
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionDec 8, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74396.png

Downloads & links

-
Map

FileDownload / File: emd_74396.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 205. Å		1.03 Å/pix.
x 200 pix.
= 205. Å		1.03 Å/pix.
x 200 pix.
= 205. 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: 0.1
Minimum - Maximum-0.038363703 - 1.920023
Average (Standard dev.)0.0031902078 (±0.04189429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 205.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_74396_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_74396_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_74396_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_74396_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 106N32 nucleosome

EntireName: 106N32 nucleosome
Components
  • Complex: 106N32 nucleosome
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: DNA (285-MER)
    • DNA: DNA (285-MER)

-
Supramolecule #1: 106N32 nucleosome

SupramoleculeName: 106N32 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

-
Macromolecule #1: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.907163 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSKSK

UniProtKB: Histone H2A type 1

-
Macromolecule #2: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

-
Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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

-
Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

-
Macromolecule #5: DNA (285-MER)

MacromoleculeName: DNA (285-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 87.851664 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DC) (DG)(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DA)(DA) (DG)(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DG) (DG)(DG)(DC)(DG)(DC)(DG)(DT)(DT)(DC)(DG) (DT) (DC)(DC)(DT)(DC)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DC) (DG)(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DA)(DA) (DG)(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DG) (DG)(DG)(DC)(DG)(DC)(DG)(DT)(DT)(DC)(DG) (DT) (DC)(DC)(DT)(DC)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DC)(DG)(DC)(DG)(DG)(DC) (DG)(DC) (DG)(DA)(DG)(DT)(DT)(DT)(DC) (DA)(DG)(DG)(DC)(DA)(DG)(DC)(DG)(DC)(DT) (DG)(DC)(DG) (DT)(DC)(DC)(DT)(DG)(DC) (DT)(DG)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DG)(DG)(DA)(DA) (DG)(DC)(DC)(DC)(DT) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DG) (DC)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA)(DA)(DT)(DT)(DG)(DG) (DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DG) (DC)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT) (DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT) (DA)(DT)(DG)(DT)(DA)(DC)(DA)(DT) (DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT)(DC)(DC) (DC)(DC) (DG)(DG)(DG)(DT)(DA)(DC)(DC) (DG)(DA)(DG)(DC)(DT)(DC)(DG)(DA)(DA)(DT) (DT)(DC)(DA) (DC)(DT)(DG)(DG)(DC)

-
Macromolecule #6: DNA (285-MER)

MacromoleculeName: DNA (285-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 88.19093 KDa
SequenceString: (DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DG) (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DG) (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DC)(DA)(DT)(DA) ...String:
(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DG) (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DG) (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DC)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT)(DA)(DG)(DC)(DT) (DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT) (DG)(DC) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DC) (DA) (DG)(DG)(DG)(DC)(DT)(DT)(DC)(DC)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DC)(DA)(DG) (DC)(DA)(DG)(DG)(DA)(DC)(DG)(DC)(DA)(DG) (DC)(DG)(DC)(DT)(DG)(DC)(DC)(DT)(DG)(DA) (DA)(DA)(DC)(DT)(DC)(DG)(DC)(DG)(DC) (DC)(DG)(DC)(DG)(DA)(DG)(DG)(DA)(DG)(DA) (DG) (DG)(DG)(DA)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DC) (DC)(DA) (DC)(DC)(DC)(DC)(DC)(DT)(DT) (DA)(DT)(DA)(DT)(DA)(DG)(DG)(DC)(DG)(DC) (DC)(DC)(DT) (DT)(DC)(DG)(DA)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Negative stain reconstruction
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 93703
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more