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- PDB-8pp6: human RYBP-PRC1 bound to H2AK118ub1 nucleosome -

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Basic information

Entry
Database: PDB / ID: 8pp6
Titlehuman RYBP-PRC1 bound to H2AK118ub1 nucleosome
Components
  • (DNA (215-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3 (Fragment)
  • Histone H4
  • RING1 and YY1-binding protein
  • Ubiquitin-40S ribosomal protein S27a (Fragment)
KeywordsGENE REGULATION / ncPRC1 / RYBP-PRC1 / nucleosome / H2A / histones / RYBP / Ubiquitin / K119
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape ...Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosomal DNA binding / transcription coregulator activity / heterochromatin formation / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / chromosome / nucleic acid binding / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / S27a-like superfamily ...Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / S27a-like superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H3 / Ubiquitin-40S ribosomal protein S27a / Histone H2B / Histone H2A / RING1 and YY1-binding protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsCiapponi, M. / Benda, C. / Mueller, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1.
Authors: Maria Ciapponi / Elena Karlukova / Sven Schkölziger / Christian Benda / Jürg Müller /
Abstract: Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified ...Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.
History
DepositionJul 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3 (Fragment)
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3 (Fragment)
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (215-MER)
J: DNA (215-MER)
K: RING1 and YY1-binding protein
M: Ubiquitin-40S ribosomal protein S27a (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,32013
Polymers294,25512
Non-polymers651
Water00
1


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

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Components

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Protein , 6 types, 10 molecules AEBFCGDHKM

#1: Protein Histone H3 (Fragment)


Mass: 15289.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: H3_1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7L0PXJ3
#2: Protein Histone H4


Mass: 11521.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4KFZ9
#3: Protein Histone H2A


Mass: 13257.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
Production host: Escherichia coli (E. coli) / References: UniProt: P84051
#4: Protein Histone H2B


Mass: 13709.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910
Production host: Escherichia coli (E. coli) / References: UniProt: P02283
#7: Protein RING1 and YY1-binding protein / Apoptin-associating protein 1 / APAP-1 / Death effector domain-associated factor / DED-associated ...Apoptin-associating protein 1 / APAP-1 / Death effector domain-associated factor / DED-associated factor / YY1 and E4TF1-associated factor 1


Mass: 25219.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYBP, DEDAF, YEAF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N488
#8: Protein Ubiquitin-40S ribosomal protein S27a (Fragment)


Mass: 8305.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli (E. coli) / References: UniProt: J3QTR3

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (215-MER)


Mass: 76456.594 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 (215-MER)


Mass: 76716.836 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, 1 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

Component
IDNameTypeEntity IDParent-IDSource
1human RYBP-PRC1 bound to H2AK118ub1 nucleosomeCOMPLEX#1-#80RECOMBINANT
2human RYBPCOMPLEX#71RECOMBINANT
3Drosophila octamerCOMPLEX#1-#41RECOMBINANT
4DNACOMPLEX#5-#61RECOMBINANT
5Human UbiquitinCOMPLEX#81RECOMBINANT
Molecular weight
IDEntity assembly-IDUnitsExperimental value
11KILODALTONS/NANOMETERNO
22
33
44
55
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Drosophila melanogaster (fruit fly)7227
54Homo sapiens (human)9606
65Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
32Trichoplusia ni (cabbage looper)7111
43Escherichia coli (E. coli)562
54Escherichia coli (E. coli)562
65Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 500 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10RELION3.1.1initial Euler assignment
11RELION3.1.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12150042 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514185
ELECTRON MICROSCOPYf_angle_d0.55920483
ELECTRON MICROSCOPYf_dihedral_angle_d29.5034099
ELECTRON MICROSCOPYf_chiral_restr0.0352327
ELECTRON MICROSCOPYf_plane_restr0.0041513

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