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- PDB-2h0d: Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex -

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Basic information

Entry
Database: PDB / ID: 2h0d
TitleStructure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex
Components
  • B lymphoma Mo-MLV insertion region
  • Ubiquitin ligase protein RING2
KeywordsMETAL BINDING PROTEIN/LIGASE / Polycomb / chromatin / ubiquitin ligase / histone / transcription / wpigenetics / METAL BINDING PROTEIN-LIGASE COMPLEX
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / rostrocaudal neural tube patterning / segment specification / ubiquitin-protein transferase activator activity / embryonic skeletal system morphogenesis / somatic stem cell division ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / PRC1 complex / sex chromatin / 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 / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / hemopoiesis / humoral immune response / negative regulation of apoptotic signaling pathway / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / Regulation of PTEN gene transcription / promoter-specific chromatin binding / brain development / RING-type E3 ubiquitin transferase / euchromatin / negative regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / ubiquitin protein ligase activity / mitotic cell cycle / gene expression / 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 / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger ...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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polycomb complex protein BMI-1 / Polycomb complex protein BMI-1 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsXu, R.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of a Bmi-1-Ring1B Polycomb Group Ubiquitin Ligase Complex.
Authors: Li, Z. / Cao, R. / Wang, M. / Myers, M.P. / Zhang, Y. / Xu, R.M.
History
DepositionMay 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B lymphoma Mo-MLV insertion region
B: Ubiquitin ligase protein RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1096
Polymers22,8472
Non-polymers2624
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-27 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.514, 120.514, 27.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein B lymphoma Mo-MLV insertion region


Mass: 11371.509 Da / Num. of mol.: 1 / Fragment: residues 5-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-KG-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5T8Z3, UniProt: P35226*PLUS
#2: Protein Ubiquitin ligase protein 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: 11475.502 Da / Num. of mol.: 1 / Fragment: residues 15-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCDFDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Tris, 500 mM NaCl, 1 mM EDTA, 1.5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2821, 1.2826, 1.25
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2005
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28211
21.28261
31.251
Reflection

D res low: 50 Å / % possible obs: 98.4

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs
4121.6317170.0751.682.57967
4221.6317170.0751.682.57967
3.5318.8227790.0771.492.76490
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.38508810.0712.273.2
4.275.3898.310.0682.1673.7
3.734.2799.310.0652.473.9
3.393.7399.210.0642.1583.9
3.153.3999.610.071.9064.2
2.963.1510010.0921.5564.1
2.822.9610010.1051.3374.2
2.692.8210010.1191.2114.1
2.592.6910010.1411.0964.2
2.52.5910010.1650.964.1
5.38508820.0712.273.2
4.275.3898.320.0682.1673.7
3.734.2799.320.0652.473.9
3.393.7399.220.0642.1583.9
3.153.3999.620.071.9064.2
2.963.1510020.0921.5564.1
2.822.9610020.1051.3374.2
2.692.8210020.1191.2114.1
2.592.6910020.1411.0964.2
2.52.5910020.1650.964.1
5.815085.730.0792.5523.1
4.625.8199.430.0622.6573.3
4.034.6299.830.062.1633.5
3.664.0310030.0611.8393.6
3.43.6699.830.0731.453.5
3.23.410030.0951.1623.7
3.043.210030.1310.9963.5
2.913.0410030.1620.8763.7
2.82.9110030.2220.8113.6
2.72.810030.2520.7513.6
ReflectionResolution: 2.5→50 Å / Num. obs: 8143 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.258 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.28263.87-4.97
13 wavelength21.28215.99-13.17
13 wavelength31.254.973.46
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Zn45.8250.3520.480.4930.548
2Zn21.0770.2550.4710.1390.359
3Zn38.3620.4390.310.2220.357

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MADNESSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→104.26 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.127 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.625 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 373 4.6 %RANDOM
Rwork0.20971 ---
obs0.21137 7686 99.04 %-
all-8143 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→104.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 4 31 1624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9962198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8345195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21522.61565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28315315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6081514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2679
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21120
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.216
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_it0.5981.51013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07621623
X-RAY DIFFRACTIONr_scbond_it2.2513683
X-RAY DIFFRACTIONr_scangle_it2.9854.5575
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 25 -
Rwork0.231 536 -
obs--99.29 %
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)
12.2202-1.80010.24412.4586-0.29332.41470.0576-0.0312-0.0468-0.1241-0.00120.0240.0112-0.1334-0.05650.04060.0081-0.00560.06130.00370.02725.928548.4712.2762
21.85650.3660.45744.22030.41382.42050.0282-0.150.12630.1692-0.0828-0.4760.03940.19860.05460.02120.01910.02070.06320.0482-0.016814.383548.77319.9753
39.2469-0.49010.20011.50890.84821.27660.3391-0.2993-0.395-0.0391-0.09510.03910.1695-0.0032-0.244-0.0183-0.0924-0.02450.10980.02870.0773-8.166138.030715.0633
45.49915.82423.419914.3035.53173.78910.0026-0.2446-0.0540.3445-0.1767-0.0496-0.13130.33940.17410.03740.018-0.00630.14720.01930.002917.751649.363328.5807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 821 - 78
2X-RAY DIFFRACTION2BB15 - 391 - 25
3X-RAY DIFFRACTION3BB40 - 11426 - 100
4X-RAY DIFFRACTION4AA83 - 10179 - 97

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