[English] 日本語
Yorodumi
- PDB-9pm0: nucleosome containing histone variant macroH2A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9pm0
Titlenucleosome containing histone variant macroH2A
Components
  • (DNA Widom601 (208bp) ...) x 2
  • Core histone macro-H2A.1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • scFv20
KeywordsDNA BINDING PROTEIN / complex / histone / DNA / nucleosome / chromatin
Function / homology
Function and homology information


negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / double-stranded methylated DNA binding ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / double-stranded methylated DNA binding / positive regulation of endodermal cell differentiation / regulation of oxidative phosphorylation / establishment of protein localization to chromatin / Barr body / sex chromatin / rDNA binding / dosage compensation by inactivation of X chromosome / poly-ADP-D-ribose modification-dependent protein binding / positive regulation of keratinocyte differentiation / negative regulation of response to oxidative stress / nucleosomal DNA binding / protein poly-ADP-ribosylation / nuclear chromosome / negative regulation of gene expression, epigenetic / regulation of lipid metabolic process / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / site of DNA damage / condensed chromosome / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...Core histone macro-H2A / Core histone macro-H2A, macro domain / : / 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 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Core histone macro-H2A.1 / Histone H2B 1.1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Mus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan, D. / Sokolova, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942049 United States
CitationJournal: To Be Published
Title: nucleosome containing histone variant macroH2A
Authors: Tan, D. / Sokolova, V.
History
DepositionJul 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Core histone macro-H2A.1
E: Core histone macro-H2A.1
B: Histone H2B 1.1
F: Histone H2B 1.1
C: Histone H3.2
G: Histone H3.2
D: Histone H4
H: Histone H4
I: DNA Widom601 (208bp) strand1
J: DNA Widom601 (208bp) strand2
M: scFv20
N: scFv20


Theoretical massNumber of molelcules
Total (without water)302,46912
Polymers302,46912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Core histone macro-H2A.1 / Histone macroH2A1 / mH2A1 / Histone H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


Mass: 17251.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MACROH2A1, H2AFY / Production host: Escherichia coli (E. coli) / References: UniProt: O75367
#2: Protein Histone H2B 1.1 / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#3: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
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
#4: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799

-
DNA Widom601 (208bp) ... , 2 types, 2 molecules IJ

#5: DNA chain DNA Widom601 (208bp) strand1


Mass: 63988.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA Widom601 (208bp) strand2


Mass: 64456.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Antibody , 1 types, 2 molecules MN

#7: Antibody scFv20


Mass: 29345.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: nucleosome containing histone variant macroH2A / Type: COMPLEX
Details: human histone variant macroH2A containing the histone fold and the linker domains
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 magnification: 81000 X / Nominal defocus max: -2000 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.27 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

-
Processing

EM software
IDNameVersionCategory
1Topaz3particle selection
2EPU9.03image acquisition
4CTFFIND4CTF correction
7PHENIX8model fitting
9EMAN2initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13PHENIX8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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