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- PDB-2ckl: Ring1b-Bmi1 E3 catalytic domain structure -

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Basic information

Entry
Database: PDB / ID: 2ckl
TitleRing1b-Bmi1 E3 catalytic domain structure
Components
  • POLYCOMB GROUP RING FINGER PROTEIN 4
  • UBIQUITIN LIGASE PROTEIN RING2
KeywordsTRANSCRIPTION / BMI1 / LIGASE / RING1B / POLYCOMB / E3-LIGASE / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / METAL-BINDING / PROTO-ONCOGENE / CHROMATIN REGULATOR / UBL CONJUGATION PATHWAY / REPRESSOR / ZINC-FINGER / RING DOMAIN / TRANSCRIPTION REGULATION COMPLEX
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / histone H2AK119 ubiquitin ligase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / PRC1 complex / RING-like zinc finger domain binding / regulation of kidney development ...Transcriptional Regulation by E2F6 / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / histone H2AK119 ubiquitin ligase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / PRC1 complex / RING-like zinc finger domain binding / regulation of kidney development / rostrocaudal neural tube patterning / hematopoietic stem cell homeostasis / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / regulation of adaxial/abaxial pattern formation / embryonic skeletal system development / sex chromatin / positive regulation of immature T cell proliferation in thymus / PcG protein complex / gastrulation with mouth forming second / anterior/posterior axis specification / positive regulation of ubiquitin-protein transferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / germ cell development / humoral immune response / hemopoiesis / MLL1 complex / negative regulation of apoptotic signaling pathway / cellular response to interleukin-1 / ubiquitin ligase complex / heterochromatin / positive regulation of B cell proliferation / cellular response to dexamethasone stimulus / epigenetic regulation of gene expression / skeletal system development / apoptotic signaling pathway / promoter-specific chromatin binding / euchromatin / brain development / RING-type E3 ubiquitin transferase / positive regulation of fibroblast proliferation / ubiquitin protein ligase activity / mitotic cell cycle / chromatin organization / in utero embryonic development / gene expression / protein ubiquitination / nuclear body / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / 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
IODIDE ION / Polycomb complex protein BMI-1 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBuchwald, G. / van der Stoop, P. / Weichenrieder, O. / Perrakis, A. / van Lohuizen, M. / Sixma, T.K.
CitationJournal: Embo J. / Year: 2006
Title: Structure and E3-Ligase Activity of the Ring-Ring Complex of Polycomb Proteins Bmi1 and Ring1B.
Authors: Buchwald, G. / Van Der Stoop, P. / Weichenrieder, O. / Perrakis, A. / Van Lohuizen, M. / Sixma, T.K.
History
DepositionApr 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYCOMB GROUP RING FINGER PROTEIN 4
B: UBIQUITIN LIGASE PROTEIN RING2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7698
Polymers31,2532
Non-polymers5156
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.046, 120.046, 27.096
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 POLYCOMB GROUP RING FINGER PROTEIN 4 / BMI1 / POLYCOMB COMPLEX PROTEIN BMI-1


Mass: 12525.765 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYS S / References: UniProt: P25916
#2: Protein UBIQUITIN LIGASE PROTEIN RING2 / RING1B / RING FINGER PROTEIN 2 / RING FINGER PROTEIN 1B


Mass: 18727.543 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTE PLYSS
References: UniProt: Q9CQJ4, 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: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPONENT OF THE POLYCOMB GROUP (PCG) MULTIPROTEIN PRC1 COMPLEX, A COMPLEX REQUIRED TO MAINTAIN THE ...COMPONENT OF THE POLYCOMB GROUP (PCG) MULTIPROTEIN PRC1 COMPLEX, A COMPLEX REQUIRED TO MAINTAIN THE TRANSCRIPTIONALLY REPRESSIVE STATE OF MANY GENES, INCLUDING HOX GENES, THROUGHOUT DEVELOPMENT. E3 UBIQUITIN LIGASE PROTEIN THAT MEDIATES MONOUBIQUITINATION OF LYS-119 OF HISTONE H2A, THEREBY PLAYING A CENTRAL ROLE IN HISTONE CODE AND GENE REGULATION

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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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growpH: 7.5
Details: 10% PEG3350, 0.1M NAI, 0.05M BIS-TRIS-PROPANE PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 16, 2004
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 15568 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.275 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 781 5 %RANDOM
Rwork0.179 ---
obs0.181 14759 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 6 123 1691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9882143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.622.81264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66215310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8341513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021137
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2802
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21120
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.5981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48121590
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3043652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.554.5553
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 52
Rwork0.207 1065
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)
13.1434-0.97221.60531.9978-1.05585.24310.0303-0.0362-0.1745-0.1161-0.01620.11620.0418-0.0749-0.014-0.26570.02090.0152-0.2271-0.0039-0.23278.37949.1550.593
292.91693.06851.07740.67821.80370.3213-0.0949-0.535-0.016-0.0860.15030.332-0.3235-0.2353-0.0195-0.07570.0002-0.02490.0012-0.0139-2.86142.0621.152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 101
2X-RAY DIFFRACTION2B15 - 38
3X-RAY DIFFRACTION2B44 - 113

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