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- PDB-3ixs: Ring1B C-terminal domain/RYBP C-terminal domain Complex -

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Basic information

Entry
Database: PDB / ID: 3ixs
TitleRing1B C-terminal domain/RYBP C-terminal domain Complex
Components
  • E3 ubiquitin-protein ligase RING2
  • RING1 and YY1-binding protein
KeywordsPROTEIN BINDING / RING1B / RYBP / polycomb / e3-ligase / chromosomal protein / transcription regulation / chromatin regulator / transcription repressor / Ligase / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription / Ubl conjugation pathway / Zinc-finger / Apoptosis / DNA-binding
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / transcription coregulator activity / euchromatin / RING-type E3 ubiquitin transferase / negative regulation of DNA-binding transcription factor activity / transcription corepressor activity / ubiquitin protein ligase activity / mitotic cell cycle / gene expression / Oxidative Stress Induced Senescence / nucleic acid binding / protein ubiquitination / nuclear body / chromatin remodeling / positive regulation of apoptotic process / apoptotic process / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / 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 / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
RING1 and YY1-binding protein / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsWang, R. / Taylor, A.B. / Kim, C.A.
CitationJournal: Structure / Year: 2010
Title: Polycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain.
Authors: Wang, R. / Taylor, A.B. / Leal, B.Z. / Chadwell, L.V. / Ilangovan, U. / Robinson, A.K. / Schirf, V. / Hart, P.J. / Lafer, E.M. / Demeler, B. / Hinck, A.P. / McEwen, D.G. / Kim, C.A.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RING2
B: RING1 and YY1-binding protein
C: E3 ubiquitin-protein ligase RING2
D: RING1 and YY1-binding protein
E: E3 ubiquitin-protein ligase RING2
F: RING1 and YY1-binding protein
G: E3 ubiquitin-protein ligase RING2
H: RING1 and YY1-binding protein
I: E3 ubiquitin-protein ligase RING2
J: RING1 and YY1-binding protein
K: E3 ubiquitin-protein ligase RING2
L: RING1 and YY1-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,78717
Polymers100,33112
Non-polymers4565
Water7,584421
1
A: E3 ubiquitin-protein ligase RING2
B: RING1 and YY1-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7843
Polymers16,7222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area8040 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase RING2
D: RING1 and YY1-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9914
Polymers16,7222
Non-polymers2692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-4 kcal/mol
Surface area8860 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase RING2
F: RING1 and YY1-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7843
Polymers16,7222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area7810 Å2
MethodPISA
4
G: E3 ubiquitin-protein ligase RING2
H: RING1 and YY1-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7843
Polymers16,7222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-7 kcal/mol
Surface area8070 Å2
MethodPISA
5
I: E3 ubiquitin-protein ligase RING2
J: RING1 and YY1-binding protein


Theoretical massNumber of molelcules
Total (without water)16,7222
Polymers16,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-10 kcal/mol
Surface area7530 Å2
MethodPISA
6
K: E3 ubiquitin-protein ligase RING2
L: RING1 and YY1-binding protein


Theoretical massNumber of molelcules
Total (without water)16,7222
Polymers16,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.894, 56.549, 100.352
Angle α, β, γ (deg.)100.88, 90.61, 100.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
E3 ubiquitin-protein ligase RING2 / RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein ...RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3


Mass: 12614.207 Da / Num. of mol.: 6 / Fragment: C-terminal Domain (UNP residues 223-333) / Mutation: N306D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAP1, DING, HIPI3, RING1B, RNF2 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide
RING1 and YY1-binding protein / Death effector domain-associated factor / DED-associated factor / YY1 and E4TF1-associated factor 1 ...Death effector domain-associated factor / DED-associated factor / YY1 and E4TF1-associated factor 1 / Apoptin-associating protein 1 / APAP-1


Mass: 4107.693 Da / Num. of mol.: 6 / Fragment: C-terminal domain (UNP residues 145-179)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEDAF, RYBP, YEAF1 / Plasmid: pET-ZL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N488
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 32% PEG 1750, 0.125 M lithium sulfate, 10% ethylene glycol, 50 mM CHES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9790, 0.9795, 1.0000
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 9, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97951
311
ReflectionResolution: 1.7→40.68 Å / Num. obs: 84818 / % possible obs: 95.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 7211 / Rsym value: 0.461 / % possible all: 83

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.4_4)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→40.676 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 4271 5.04 %RANDOM
Rwork0.203 ---
obs0.2045 84786 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.4373 Å2-0.9697 Å22.5008 Å2
2---1.553 Å2-3.7215 Å2
3----0.2752 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 29 421 6923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066615
X-RAY DIFFRACTIONf_angle_d1.068941
X-RAY DIFFRACTIONf_dihedral_angle_d15.252440
X-RAY DIFFRACTIONf_chiral_restr0.0681053
X-RAY DIFFRACTIONf_plane_restr0.0041114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.2611960.25942140X-RAY DIFFRACTION74
1.7193-1.73960.27611330.25252195X-RAY DIFFRACTION81
1.7396-1.76080.28721280.25372652X-RAY DIFFRACTION94
1.7608-1.78310.27711340.24462666X-RAY DIFFRACTION95
1.7831-1.80650.24091230.22492737X-RAY DIFFRACTION96
1.8065-1.83130.25631450.22112698X-RAY DIFFRACTION97
1.8313-1.85740.25811310.21812669X-RAY DIFFRACTION96
1.8574-1.88520.27431690.22532749X-RAY DIFFRACTION96
1.8852-1.91460.27361540.23432611X-RAY DIFFRACTION96
1.9146-1.9460.26461550.22452724X-RAY DIFFRACTION97
1.946-1.97960.2221330.21412708X-RAY DIFFRACTION97
1.9796-2.01550.24121510.20582720X-RAY DIFFRACTION97
2.0155-2.05430.24051180.20942717X-RAY DIFFRACTION97
2.0543-2.09620.24291380.20972777X-RAY DIFFRACTION97
2.0962-2.14180.24941660.20572662X-RAY DIFFRACTION97
2.1418-2.19160.25981650.20412697X-RAY DIFFRACTION97
2.1916-2.24640.2911280.21372747X-RAY DIFFRACTION97
2.2464-2.30720.26121620.20062692X-RAY DIFFRACTION98
2.3072-2.37510.24281490.20032771X-RAY DIFFRACTION98
2.3751-2.45170.24411500.20372724X-RAY DIFFRACTION98
2.4517-2.53930.22911490.20532745X-RAY DIFFRACTION98
2.5393-2.6410.22321460.21112713X-RAY DIFFRACTION98
2.641-2.76120.27681390.2082765X-RAY DIFFRACTION98
2.7612-2.90670.26131420.21692770X-RAY DIFFRACTION98
2.9067-3.08870.24631490.21172761X-RAY DIFFRACTION99
3.0887-3.32710.23571630.19662739X-RAY DIFFRACTION99
3.3271-3.66180.24891450.1922739X-RAY DIFFRACTION98
3.6618-4.19120.19251410.17552760X-RAY DIFFRACTION98
4.1912-5.27860.16171220.16392752X-RAY DIFFRACTION98
5.2786-40.68810.20831470.20852715X-RAY DIFFRACTION97

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