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- PDB-6wi8: Inhibitor compound-induced confrontational change in Ring1b-Bmi1 ... -

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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 / regulation of kidney development / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / positive regulation of immature T cell proliferation in thymus ...regulation of adaxial/abaxial pattern formation / RING-like zinc finger domain binding / PRC1 complex / regulation of kidney development / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / positive regulation of immature T cell proliferation in thymus / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / DNA methylation-dependent constitutive heterochromatin formation / 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 / cellular response to interleukin-1 / ubiquitin ligase complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / positive regulation of B cell proliferation / cellular response to dexamethasone stimulus / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / brain development / RING-type E3 ubiquitin transferase / positive regulation of fibroblast proliferation / transferase activity / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / protein ubiquitination / chromatin remodeling / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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.: 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

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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: 2.26 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

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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

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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

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