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- PDB-6wi7: RING1B-BMI1 fusion in closed conformation -

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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 / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex ...: / regulation of adaxial/abaxial pattern formation / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / PRC1 complex / segment specification / 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 / MLL1 complex / hemopoiesis / 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 / metal ion binding / nucleus / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / 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 / Glycerol


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


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

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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: 2.33 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

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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

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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

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