[English] 日本語
Yorodumi
- PDB-6wi8: Inhibitor compound-induced confrontational change in Ring1b-Bmi1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wi8
TitleInhibitor compound-induced confrontational change in Ring1b-Bmi1 domain structure
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 / 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 ...regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / 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 / 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 / hemopoiesis / negative regulation of apoptotic signaling pathway / humoral immune response / 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 / apoptotic signaling pathway / promoter-specific chromatin binding / 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 / protein ubiquitination / 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 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 / MOLECULAR REPLACEMENT / Resolution: 3.092 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 9, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,16910
Polymers48,6452
Non-polymers5238
Water905
1
A: E3 ubiquitin-protein ligase RING2,Polycomb complex protein BMI-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5845
Polymers24,3231
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RING2,Polycomb complex protein BMI-1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5845
Polymers24,3231
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.081, 154.742, 49.579
Angle α, β, γ (deg.)90.000, 92.260, 90.000
Int Tables number4
Space group name H-MP1211

-
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.: 2
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.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM acetate, pH 4.5, 200 mM lithium sulfate, 2.5 M sodium chloride

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 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: 3.09→50 Å / Num. obs: 7292 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rsym value: 0.11 / Net I/σ(I): 13.28
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 7320 / Rsym value: 0.443

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WI7

6wi7


Resolution: 3.092→41.721 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.15
RfactorNum. reflection% reflection
Rfree0.2588 726 9.96 %
Rwork0.2066 --
obs0.2119 7292 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.19 Å2 / Biso mean: 65.5982 Å2 / Biso min: 17.04 Å2
Refinement stepCycle: final / Resolution: 3.092→41.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 8 5 3166
Biso mean--60.94 21.06 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023215
X-RAY DIFFRACTIONf_angle_d0.5414356
X-RAY DIFFRACTIONf_chiral_restr0.041517
X-RAY DIFFRACTIONf_plane_restr0.004544
X-RAY DIFFRACTIONf_dihedral_angle_d12.2691998
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.33010.33521380.262123993
3.3301-3.66510.3231360.2278130597
3.6651-4.1950.24971520.21133799
4.195-5.28360.23741490.1829133899
5.2836-41.70.23011510.1951134799
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)
12.6781.3545-0.06937.59131.16174.3071-0.15310.1798-0.2719-0.7664-0.4491-0.5020.7940.00650.46460.44470.01460.09770.43520.01880.484611.36842.1855-5.0141
26.8423-1.5745-0.97424.1728-2.7276.6846-0.0632-0.4992-0.41940.7612-0.15870.30651.21660.48750.07170.8729-0.0166-0.05340.36730.04110.3347.6727-13.318413.646
32.33320.4949-0.03192.366-1.99788.906-0.1817-0.23410.0418-0.1453-0.01750.64051.9427-0.681-0.09160.4279-0.10280.08210.5012-0.07790.47422.9788-9.54630.7064
43.87462.3419-1.02192.92120.74592.6572-0.10420.44180.03530.1111-0.04050.12710.0116-0.07750.15740.13640.0437-0.03870.31640.01640.32956.82936.79651.2332
55.50922.45313.49648.14590.46752.57370.32080.4467-0.08220.60160.03560.04870.0652-0.5365-0.2070.29570.01230.06810.49140.07610.28156.632226.165829.8199
68.1651-0.3414-5.11325.30557.47942.0010.6343-0.19621.4513-1.12980.7333-0.5668-3.76863.9374-1.66670.8835-0.23530.14621.199-0.38631.09059.413351.317127.3375
78.06332.5260.07795.7523-1.80920.6812-0.21550.86810.5691-1.2174-0.3158-0.2102-2.03530.07230.31851.6886-0.1101-0.23340.59840.07090.68244.300349.884210.885
81.4910.5252-1.35323.86690.26785.9162-0.6319-0.01960.1648-0.4402-0.56751.0441-0.83540.30760.35630.48910.0691-0.19150.42980.1230.57290.911946.883922.1037
92.5365-1.04420.7344.52761.69013.2047-0.10310.0424-0.0667-0.1817-0.31120.4138-0.2649-0.21150.39660.2636-0.00050.08770.3879-0.03680.36373.17830.407523.8144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 49 )A15 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 91 )A50 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 1015 )A92 - 1015
4X-RAY DIFFRACTION4chain 'A' and (resid 1016 through 1102 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 36 )B16 - 36
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 54 )B37 - 54
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 90 )B55 - 90
8X-RAY DIFFRACTION8chain 'B' and (resid 91 through 1011 )B91 - 1011
9X-RAY DIFFRACTION9chain 'B' and (resid 1012 through 1102 )B0

+
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