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- PDB-5fr6: The structure of polycomb ULD complex -

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Basic information

Entry
Database: PDB / ID: 5fr6
TitleThe structure of polycomb ULD complex
ComponentsPOLYCOMB COMPLEX PROTEIN BMI-1
KeywordsTRANSCRIPTION / BMI1 / POLYCOMB / PHC2
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 / apoptotic signaling pathway / Regulation of PTEN gene transcription / promoter-specific chromatin binding / 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 / nucleus / cytosol
Similarity search - Function
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) ...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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Polycomb complex protein BMI-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsGray, F. / Cho, H.J. / Cierpicki, T.
CitationJournal: Nat.Commun. / Year: 2016
Title: Bmi1 Regulates Prc1 Architecture and Activity Through Homo-and Hetero-Oligomerization
Authors: Gray, F. / Cho, H.J. / Shihan, S. / Harris, A. / Boytsov, B. / Jaremko, L. / Jaremko, M. / Demeler, B. / Lawlor, E.R. / Grembecka, J. / Cierpicki, T.
History
DepositionDec 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYCOMB COMPLEX PROTEIN BMI-1


Theoretical massNumber of molelcules
Total (without water)14,0981
Polymers14,0981
Non-polymers00
Water57632
1
A: POLYCOMB COMPLEX PROTEIN BMI-1

A: POLYCOMB COMPLEX PROTEIN BMI-1


Theoretical massNumber of molelcules
Total (without water)28,1972
Polymers28,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area920 Å2
ΔGint-10.1 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.275, 78.275, 43.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

#1: Protein POLYCOMB COMPLEX PROTEIN BMI-1 / BMI1 / OLYCOMB GROUP RING FINGER PROTEIN 4 / RING FINGER PROTEIN 51


Mass: 14098.457 Da / Num. of mol.: 1 / Fragment: POLYCOMB COMPLEX, UNP RESIDUES 121-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 / References: UniProt: P35226
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.95 Å3/Da / Density % sol: 58.29 % / Description: NONE
Crystal growpH: 6.5
Details: 100MM MES, PH 6.5, 50MM MGCL2, 7% ISOPROPANOL, 6% PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2014
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 5292 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 33.93
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.27 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HPM

4hpm


Resolution: 2.51→39.14 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.847 / SU B: 11.072 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CO-CRYSTALLIZED WITH PHC2 33-56 PEPTIDE. UNX DENSITY IS A HALF PERCENT OF PHC2 PEPTIDE. WE CONFIRMED THIS STRUCTURE BY NMR EXPERIMENT TOGETHER
RfactorNum. reflection% reflectionSelection details
Rfree0.32833 267 5.1 %RANDOM
Rwork0.23253 ---
obs0.23748 5015 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.51→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms692 0 0 32 724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02710
X-RAY DIFFRACTIONr_bond_other_d0.0060.02672
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.986961
X-RAY DIFFRACTIONr_angle_other_deg1.14431549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.121581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72722.81232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00715126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.066155
X-RAY DIFFRACTIONr_chiral_restr0.0940.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021760
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02159
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it8.32410.377330
X-RAY DIFFRACTIONr_mcbond_other8.31910.359329
X-RAY DIFFRACTIONr_mcangle_it10.74919.41409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.72612.026380
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it13.87821.598553
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: 2.507→2.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 5 -
Rwork0.248 380 -
obs--97.96 %

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