[English] 日本語
Yorodumi
- PDB-3h8h: Structure of the C-terminal domain of human RNF2/RING1B; -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h8h
TitleStructure of the C-terminal domain of human RNF2/RING1B;
ComponentsE3 ubiquitin-protein ligase RING2
KeywordsTRANSCRIPTION / UBIQUITIN FOLD / LIGASE / RING1B / POLYCOMB / E3-LIGASE / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / METAL-BINDING / PROTO-ONCOGENE / CHROMATIN REGULATOR / UBL CONJUGATION PATHWAY / REPRESSOR / TRANSCRIPTION REGULATION COMPLEX / Nucleus / Phosphoprotein / Zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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 / euchromatin / RING-type E3 ubiquitin transferase / negative regulation of DNA-binding transcription factor activity / ubiquitin protein ligase activity / mitotic cell cycle / gene expression / Oxidative Stress Induced Senescence / protein ubiquitination / nuclear body / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. ...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. / 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
E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsWalker, J.R. / Bezsonova, I. / Bacik, J. / Duan, S. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Biochemistry / Year: 2009
Title: Ring1B contains a ubiquitin-like docking module for interaction with Cbx proteins.
Authors: Bezsonova, I. / Walker, J.R. / Bacik, J.P. / Duan, S. / Dhe-Paganon, S. / Arrowsmith, C.H.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2845
Polymers12,6461
Non-polymers6384
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2580 Å2
ΔGint-65 kcal/mol
Surface area10790 Å2
MethodPISA
3
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2050 Å2
ΔGint-25 kcal/mol
Surface area10950 Å2
MethodPISA
4
A: E3 ubiquitin-protein ligase RING2
hetero molecules

A: E3 ubiquitin-protein ligase RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,56910
Polymers25,2922
Non-polymers1,2768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1940 Å2
ΔGint-23 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.169, 72.169, 90.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 1 types, 1 molecules A

#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: 12646.210 Da / Num. of mol.: 1 / Fragment: RESIDUES 220-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAP1, DING, HIPI3, RING1B, RNF2 / Plasmid: PET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus
References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 2 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 7, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→27.28 Å / Num. obs: 9884 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rsym value: 0.112 / Net I/σ(I): 28.58
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.67 / Rsym value: 0.724 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SOLVEphasing
RESOLVEmodel building
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.699 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 471 4.8 %RANDOM
Rwork0.2 ---
obs0.202 9415 99.2 %-
all-9884 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 25 59 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9991062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.877595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33623.44829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84515130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.021153
X-RAY DIFFRACTIONr_chiral_restr0.120.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9241.5476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6482769
X-RAY DIFFRACTIONr_scbond_it2.5033309
X-RAY DIFFRACTIONr_scangle_it3.94.5293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 38 -
Rwork0.239 617 -
obs--92.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6260.1967-7.1444.9217-3.975517.0331-0.1039-0.60150.0030.77230.1331-0.0020.01770.0157-0.02930.2576-0.0591-0.03850.34290.00540.213419.377915.474214.5417
23.54560.64962.92813.48060.99949.2891-0.0551-0.1720.08760.20390.0378-0.1039-0.09220.07720.01730.11390.00880.00680.11420.00140.146921.153717.6368-1.4682
38.50086.7937-2.548910.35471.03616.02690.2172-0.17570.06440.115-0.0109-0.9498-0.67840.8204-0.20630.2715-0.0322-0.06380.2494-0.01780.38621.370921.3737-7.2758
46.48530.2397-3.40778.491-2.38219.74380.2324-0.224-0.14590.01180.014-0.2944-0.25651.0604-0.24640.146-0.0268-0.070.2112-0.02770.216124.817920.79767.2116
56.41162.87776.49326.5519-0.92019.6860.3835-0.47140.01910.5805-0.26930.23970.2586-0.2371-0.11420.20620.03960.03510.1924-0.01680.103711.849319.427213.575
69.91934.3011-0.361911.7495-1.55199.7643-0.0694-0.14050.00110.33670.14040.203-0.127-0.2885-0.0710.13270.0142-0.00760.1196-0.01140.128210.434624.87516.8846
79.69220.6032-1.0583.8521-0.82420.7167-0.14880.2874-0.082-0.3670.16970.0387-0.00910.1743-0.02090.2468-0.0452-0.01250.1757-0.0410.173518.774229.90513.4612
812.22084.67423.79826.8082.92665.1960.17490.08620.0395-0.08430.0094-0.1423-0.18910.281-0.18420.26820.0160.00180.25780.01720.250616.98832.0032-1.0833
94.238-1.33972.03029.3746-4.40295.634-0.06630.19590.38440.1332-0.3056-0.2074-0.25590.09890.37190.1105-0.0248-0.04020.09950.00140.120612.197920.1293-1.041
103.48881.5413-1.83283.55772.69968.74940.0060.3028-0.0949-0.1257-0.0279-0.25490.2074-0.18270.02180.14890.0167-0.00570.1492-0.02030.159516.53646.688-3.384
110.08640.37710.01913.18852.39456.48780.0429-0.00090.0571-0.1785-0.35170.67540.0908-0.64130.30880.17930.045-0.08220.1629-0.07560.25467.353515.10122.7821
1214.05961.33424.00228.75612.32524.856-0.1413-0.509-0.19750.45070.14760.11810.1039-0.1624-0.00620.1515-0.00480.01870.14950.00520.13918.603613.765811.446
136.47-1.6131-2.543315.51920.94645.547-0.0533-0.1632-0.3680.37290.04260.22340.2765-0.13380.01060.134-0.00050.01060.13940.00730.155910.56158.31218.7133
142.6983-4.51160.83848.0596-0.12583.42050.1940.0576-0.0915-0.2711-0.15210.13830.2145-0.0912-0.04190.1638-0.0161-0.05220.15670.02670.209519.9936.88799.6431
153.3267-0.22921.42321.5413-1.42249.26480.0272-0.1785-0.2027-0.10320.12670.29790.05290.0213-0.15390.11710.0081-0.01580.106-0.01840.13818.471416.47060.9077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A224 - 229
2X-RAY DIFFRACTION2A230 - 235
3X-RAY DIFFRACTION3A236 - 239
4X-RAY DIFFRACTION4A243 - 249
5X-RAY DIFFRACTION5A250 - 256
6X-RAY DIFFRACTION6A257 - 261
7X-RAY DIFFRACTION7A262 - 272
8X-RAY DIFFRACTION8A285 - 289
9X-RAY DIFFRACTION9A290 - 295
10X-RAY DIFFRACTION10A296 - 302
11X-RAY DIFFRACTION11A303 - 308
12X-RAY DIFFRACTION12A309 - 313
13X-RAY DIFFRACTION13A314 - 318
14X-RAY DIFFRACTION14A319 - 324
15X-RAY DIFFRACTION15A325 - 330

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more