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- PDB-9dby: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome -

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Basic information

Entry
Database: PDB / ID: 9dby
TitlencPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Components
  • (DNA (187-MER)) x 2
  • (Histone H2A type ...) x 2
  • E3 ubiquitin-protein ligase RING2
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Polycomb complex protein BMI-1
  • RING1 and YY1-binding protein
  • Ubiquitin
KeywordsGENE REGULATION/DNA / DNA complex protein / hydrolase / structural protein / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / rostrocaudal neural tube patterning / segment specification / ubiquitin-protein transferase activator activity / embryonic skeletal system morphogenesis / somatic stem cell division ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / rostrocaudal neural tube patterning / segment specification / ubiquitin-protein transferase activator activity / embryonic skeletal system morphogenesis / somatic stem cell division / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / negative regulation of gene expression, epigenetic / female gonad development / seminiferous tubule development / male meiosis I / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / hemopoiesis / MLL1 complex / negative regulation of apoptotic signaling pathway / humoral immune response / heterochromatin / SUMOylation of DNA damage response and repair proteins / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / positive regulation of B cell proliferation / energy homeostasis / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / epigenetic regulation of gene expression / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / SUMOylation of chromatin organization proteins / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / SUMOylation of transcription cofactors / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1
Similarity search - Function
Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / 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 domain / Zn-finger in Ran binding protein and others ...Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / 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 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / 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. / Zinc finger RING-type profile. / Histone H3 signature 2. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Polycomb complex protein BMI-1 / Histone H4 / Histone H3.2 / RING1 and YY1-binding protein / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGodinez-Lopez, V. / Valencia-Sanchez, M.I. / Armache, J.P. / Armache, K.-J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: To Be Published
Title: Structural visualization of read-write mechanisms of histone H2A lysine 119 mono-ubiquitination by Polycomb Repressive Complex 1
Authors: Godinez-Lopez, V. / Valencia-Sanchez, M.I. / Armache, J.P. / Armache, K.-J.
History
DepositionAug 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (187-MER)
J: DNA (187-MER)
K: Polycomb complex protein BMI-1
L: E3 ubiquitin-protein ligase RING2
M: RING1 and YY1-binding protein
N: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,77619
Polymers333,44914
Non-polymers3275
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 , 7 types, 10 molecules AEBFDHKLMN

#1: Protein Histone H3.2 / Histone H3


Mass: 15435.126 Da / Num. of mol.: 2 / Mutation: G103A
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
#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
#4: Protein Histone H2B 1.1


Mass: 13979.291 Da / Num. of mol.: 2 / Mutation: S33T
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
#8: 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: Escherichia coli (E. coli) / References: UniProt: P35226
#9: 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: Escherichia coli (E. coli)
References: UniProt: Q99496, RING-type E3 ubiquitin transferase
#10: 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: 24863.625 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: Escherichia coli (E. coli) / References: UniProt: Q8N488
#11: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Histone H2A type ... , 2 types, 2 molecules CG

#3: Protein Histone H2A type 1


Mass: 14093.436 Da / Num. of mol.: 1 / Mutation: G100R, K119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein Histone H2A type 1


Mass: 14067.398 Da / Num. of mol.: 1 / Mutation: G100R, K119C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (187-MER)


Mass: 57982.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (187-MER)


Mass: 57488.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 5 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Type: COMPLEX / Entity ID: #1-#4, #6-#11 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 10157

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Processing

EM software
IDNameVersionCategory
2Leginonv 3.6image acquisition
7UCSF ChimeraX1.7.1model fitting
8Coot0.9.8.94model fitting
10PHENIX1.20.1model refinement
14cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10753652
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206339 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDDetailsSource nameTypeAccession codeInitial refinement model-ID
1Multimer predictionAlphaFoldin silico model
23tu4

3tu4

PDBexperimental model3tu42
38H1T

8h1t

PDBexperimental model8H1T3
48SVF

8svf

PDBexperimental model8SVF4
54R8P

4r8p

PDBexperimental model4R8P5
62D9G

2d9g

PDBexperimental model2D9G6
7SwissModelTemplateSwissModelin silico model
81UBQ

1ubq

PDBexperimental model1UBQ8

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