[English] 日本語
Yorodumi
- PDB-6wi7: RING1B-BMI1 fusion in closed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wi7
TitleRING1B-BMI1 fusion in closed conformation
ComponentsE3 ubiquitin-protein ligase RING2, Polycomb complex protein BMI-1 chimera
KeywordsLIGASE / E3 ubiquitin ligase / Ring1b / Bmi1
Function / homology
Function and homology information


: / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex ...: / regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / MLL1 complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / brain development / positive regulation of fibroblast proliferation / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Polycomb complex protein BMI-1 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.702 Å
AuthorsCho, H.J. / Cierpicki, T.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain.
Authors: Shukla, S. / Ying, W. / Gray, F. / Yao, Y. / Simes, M.L. / Zhao, Q. / Miao, H. / Cho, H.J. / Gonzalez-Alonso, P. / Winkler, A. / Lund, G. / Purohit, T. / Kim, E. / Zhang, X. / Ray, J.M. / ...Authors: Shukla, S. / Ying, W. / Gray, F. / Yao, Y. / Simes, M.L. / Zhao, Q. / Miao, H. / Cho, H.J. / Gonzalez-Alonso, P. / Winkler, A. / Lund, G. / Purohit, T. / Kim, E. / Zhang, X. / Ray, J.M. / He, S. / Nikolaidis, C. / Ndoj, J. / Wang, J. / Jaremko, L. / Jaremko, M. / Ryan, R.J.H. / Guzman, M.L. / Grembecka, J. / Cierpicki, T.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RING2, Polycomb complex protein BMI-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9157
Polymers24,3231
Non-polymers5926
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint3 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.311, 54.353, 82.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein E3 ubiquitin-protein ligase RING2, Polycomb complex protein BMI-1 chimera / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 24322.715 Da / Num. of mol.: 1
Fragment: RING-2 (UNP residues 10-116) + BMI-1 (UNP residues 1-104)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BMI1, PCGF4, RNF51 / Plasmid: PET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X6RFN3, UniProt: P35226, Isomerases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2014 / Details: NULL
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24900 / % possible obs: 100 % / Redundancy: 6.7 % / Rsym value: 0.09 / Net I/σ(I): 24.18
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 24900 / Rsym value: 0.575

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.702→36.521 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.1957 1240 4.99 %
Rwork0.1646 --
obs0.1662 24843 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.46 Å2 / Biso mean: 25.2751 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.702→36.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 25 273 1929
Biso mean--38.5 35.9 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081715
X-RAY DIFFRACTIONf_angle_d0.9432327
X-RAY DIFFRACTIONf_chiral_restr0.059273
X-RAY DIFFRACTIONf_plane_restr0.005288
X-RAY DIFFRACTIONf_dihedral_angle_d8.1421484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.702-1.77010.32261240.2337252598
1.7701-1.85070.25261370.19242569100
1.8507-1.94820.2071470.17582593100
1.9482-2.07030.18261530.16552581100
2.0703-2.23010.18521410.15492604100
2.2301-2.45450.19581290.16332637100
2.4545-2.80950.20771270.16112630100
2.8095-3.53930.18711430.16572670100
3.5393-36.520.17861390.15332794100
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)
13.0275-0.4011-0.50220.8962-0.35670.7459-0.0603-0.00240.00620.0930.0653-0.0389-0.03790.0784-0.01550.13480.0069-0.00720.0787-0.01840.12095.48781.2442-4.2727
22.409-0.53460.69282.4771-0.59361.7378-0.075-0.1044-0.07010.12340.148-0.089-0.0432-0.0853-0.04990.08860.0230.02060.09670.00020.0943-2.3388-4.12011.3453
34.7651-2.0019-4.27112.70452.62574.1979-0.0126-0.18510.06450.15770.08510.011-0.12240.2327-0.05240.18320.04930.01030.15820.03190.1722-15.287411.04087.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 113 )A12 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 1085 )A114 - 1085
3X-RAY DIFFRACTION3chain 'A' and (resid 1086 through 1102 )A0

+
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://pdbjlvh1.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