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- PDB-9v9h: Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex -

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Basic information

Entry
Database: PDB / ID: 9v9h
TitleCryo-EM structure of the cPRC1-di-nucleosome (tight) complex
Components
  • (DNA (276-MER)) x 2
  • E3 ubiquitin-protein ligase RING2
  • Histone H2A type 1-H
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3.1
  • Histone H4
  • Polycomb complex protein BMI-1
KeywordsGENE REGULATION / nucleosome modification / transcriptional regulation
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / regulation of adaxial/abaxial pattern formation / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / regulation of adaxial/abaxial pattern formation / somatic stem cell division / embryonic skeletal system morphogenesis / sex chromatin / positive regulation of immature T cell proliferation in thymus / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / positive regulation of ubiquitin-protein transferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / germ cell development / humoral immune response / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / MLL1 complex / hemopoiesis / negative regulation of apoptotic signaling pathway / : / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / positive regulation of B cell proliferation / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / SUMOylation of transcription cofactors / Deposition of new CENPA-containing nucleosomes at the centromere / epigenetic regulation of gene expression / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / apoptotic signaling pathway / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / brain development / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of fibroblast proliferation / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / Metalloprotease DUBs / HCMV Early Events / structural constituent of chromatin / ubiquitin protein ligase activity / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / mitotic cell cycle
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2A conserved site ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Polycomb complex protein BMI-1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-H / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYu, Y. / Cai, D. / Zhang, Y.Z. / Huang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural mechanisms of PRC1-mediated interplay between gene repression and activation
Authors: Yu, Y. / Cai, D. / Zhang, Y.Z. / Huang, J.
History
DepositionMay 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-H
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-H
H: Histone H2B type 1-C/E/F/G/I
I: DNA (276-MER)
J: DNA (276-MER)
K: Histone H3.1
L: Histone H2A type 1-H
M: Histone H3.1
N: Histone H2B type 1-C/E/F/G/I
O: Histone H2A type 1-H
P: Histone H2B type 1-C/E/F/G/I
Q: Histone H4
R: Histone H4
S: Polycomb complex protein BMI-1
T: E3 ubiquitin-protein ligase RING2
U: Polycomb complex protein BMI-1
V: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,23430
Polymers538,71122
Non-polymers5238
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 , 6 types, 20 molecules AEKMBFQRCGLODHNPSUTV

#1: Protein
Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68431
#2: Protein
Histone H4


Mass: 11394.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62805
#3: Protein
Histone H2A type 1-H / H2A-clustered histone 12 / Histone H2A/s


Mass: 13935.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96KK5
#4: Protein
Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13937.213 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62807
#7: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 37006.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Homo sapiens (human) / References: UniProt: P35226
#8: Protein E3 ubiquitin-protein ligase RING2 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1 / RING-type E3 ubiquitin transferase RING2


Mass: 37706.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Homo sapiens (human)
References: UniProt: Q99496, RING-type E3 ubiquitin transferase

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (276-MER)


Mass: 85179.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#6: DNA chain DNA (276-MER)


Mass: 85290.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 1 types, 8 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: cPRC1-di-nucleosome(tight) complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 3000 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 softwareName: PHENIX / Version: 1.19.2_4122 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97701 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002927948
ELECTRON MICROSCOPYf_angle_d0.511740119
ELECTRON MICROSCOPYf_chiral_restr0.03554588
ELECTRON MICROSCOPYf_plane_restr0.0033154
ELECTRON MICROSCOPYf_dihedral_angle_d29.24367654

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