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- PDB-4hpl: PCGF1 Ub fold (RAWUL)/BCOR PUFD Complex -

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Basic information

Entry
Database: PDB / ID: 4hpl
TitlePCGF1 Ub fold (RAWUL)/BCOR PUFD Complex
Components
  • BCL-6 corepressor
  • Polycomb group RING finger protein 1
KeywordsTRANSCRIPTION / POLYCOMB / BCOR / BCL-6 CO-REPRESSOR / PCGF1 / RAWUL / NSPC1 / E3-LIGASE / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / TRANSCRIPTION REPRESSOR / LIGASE / METAL-BINDING / NUCLEUS / REPRESSOR / UBL CONJUGATION PATHWAY / ZINC-FINGER
Function / homology
Function and homology information


negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / blastocyst hatching / negative regulation of bone mineralization / PcG protein complex / odontogenesis / roof of mouth development / heat shock protein binding ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / blastocyst hatching / negative regulation of bone mineralization / PcG protein complex / odontogenesis / roof of mouth development / heat shock protein binding / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone deacetylase binding / transcription corepressor activity / heart development / DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
BCL-6 corepressor, PCGF1 binding domain / BCL-6 corepressor, non-ankyrin-repeat domain / BCL-6 co-repressor, non-ankyrin-repeat region / BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / Mlu1-box Binding Protein; DNA-binding Domain / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like ...BCL-6 corepressor, PCGF1 binding domain / BCL-6 corepressor, non-ankyrin-repeat domain / BCL-6 co-repressor, non-ankyrin-repeat region / BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / Mlu1-box Binding Protein; DNA-binding Domain / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
BCL-6 corepressor / Polycomb group RING finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJunco, S.E. / Wang, R. / Gaipa, J. / Taylor, A.B. / Gearhart, M.D. / Bardwell, V.J. / Hart, P.J. / Kim, C.A.
CitationJournal: Structure / Year: 2013
Title: Structure of the Polycomb Group Protein PCGF1 in Complex with BCOR Reveals Basis for Binding Selectivity of PCGF Homologs.
Authors: Junco, S.E. / Wang, R. / Gaipa, J.C. / Taylor, A.B. / Schirf, V. / Gearhart, M.D. / Bardwell, V.J. / Demeler, B. / Hart, P.J. / Kim, C.A.
History
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BCL-6 corepressor
B: Polycomb group RING finger protein 1


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-14 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.681, 67.681, 75.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1801-

HOH

21A-1810-

HOH

31A-1814-

HOH

41B-310-

HOH

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Components

#1: Protein BCL-6 corepressor / BCoR


Mass: 13679.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1634-1748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCOR, KIAA1575 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6W2J9
#2: Protein Polycomb group RING finger protein 1 / Nervous system Polycomb-1 / NSPc1 / RING finger protein 68 / PCGF1 Ub fold (RAWUL)


Mass: 11074.042 Da / Num. of mol.: 1 / Fragment: UNP residues 167-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSPC1, PCGF1, RNF68 / Plasmid: pet-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BSM1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 50 mM MES, 8.5% polyethylene glycol (PEG) 8000, 300 mM sodium bromide, 10% ethylene glycol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.919 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2→19.54 Å / Num. obs: 13386 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 31.8 Å2 / Rsym value: 0.069 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1949 / Rsym value: 0.586 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19.54 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 32.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1325 9.92 %random
Rwork0.2121 ---
obs0.2168 13359 99.93 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 2→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 79 1691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081647
X-RAY DIFFRACTIONf_angle_d1.1562231
X-RAY DIFFRACTIONf_dihedral_angle_d16.224619
X-RAY DIFFRACTIONf_chiral_restr0.068254
X-RAY DIFFRACTIONf_plane_restr0.005283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.35721460.31711334X-RAY DIFFRACTION100
2.0801-2.17460.33061480.26531326X-RAY DIFFRACTION100
2.1746-2.28910.30361480.24231322X-RAY DIFFRACTION100
2.2891-2.43230.2941530.2391329X-RAY DIFFRACTION100
2.4323-2.61970.32191440.24981336X-RAY DIFFRACTION100
2.6197-2.88250.33591470.23431323X-RAY DIFFRACTION100
2.8825-3.29790.2741450.21851355X-RAY DIFFRACTION100
3.2979-4.14850.25091430.19171336X-RAY DIFFRACTION100
4.1485-19.540.19641510.17831373X-RAY DIFFRACTION100

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