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- PDB-9v9x: Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI... -

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Basic information

Entry
Database: PDB / ID: 9v9x
TitleCryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome
Components
  • DNA (130-MER)
  • DNA (131-MER)
  • E3 ubiquitin-protein ligase RING2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • 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 / positive regulation of B cell proliferation / heterochromatin / SUMOylation of transcription cofactors / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / euchromatin / brain development / RING-type E3 ubiquitin transferase / positive regulation of fibroblast proliferation / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / mitotic cell cycle / heterochromatin formation / nucleosome assembly / regulation of gene expression / Oxidative Stress Induced Senescence / gene expression / in utero embryonic development / nuclear body / protein ubiquitination / chromatin remodeling / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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) / Histone H3 / Histone H2B / Polycomb complex protein BMI-1 / Histone H4 / Histone H2A / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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
DepositionJun 2, 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / 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: Mask / Part number: 1 / Data content type: Mask / 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
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (130-MER)
J: DNA (131-MER)
M: Polycomb complex protein BMI-1
N: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,24116
Polymers264,97912
Non-polymers2624
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, 10 molecules AEBFCGDHMN

#1: Protein Histone H3


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11394.426 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
#3: Protein Histone H2A


Mass: 14083.398 Da / Num. of mol.: 2 / Mutation: K119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B


Mass: 13939.228 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704304 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0TWI5
#7: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 37006.062 Da / Num. of mol.: 1
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.: 1
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 (130-MER)


Mass: 39924.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (131-MER)


Mass: 40637.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 4 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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: ncPRC1.4-NCP_H2AK119ub complex_1 RNF2-BMI1 / Type: COMPLEX
Details: The ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome
Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33390 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002613723
ELECTRON MICROSCOPYf_angle_d0.476119656
ELECTRON MICROSCOPYf_chiral_restr0.03252249
ELECTRON MICROSCOPYf_plane_restr0.00291584
ELECTRON MICROSCOPYf_dihedral_angle_d28.78043687

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