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- PDB-4hpm: PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex -

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Basic information

Entry
Database: PDB / ID: 4hpm
TitlePCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex
Components
  • BCL-6 corepressor-like protein 1
  • Polycomb group RING finger protein 1
KeywordsTRANSCRIPTION / POLYCOMB / BCORL1 / 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


PRC1 complex / PcG protein complex / promoter-specific chromatin binding / transcription corepressor activity / chromatin organization / chromatin remodeling / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm ...PRC1 complex / PcG protein complex / promoter-specific chromatin binding / transcription corepressor activity / chromatin organization / chromatin remodeling / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
BCL-6 corepressor, PCGF1 binding domain / 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 ...BCL-6 corepressor, PCGF1 binding domain / 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 / Ankyrin repeat-containing domain superfamily / 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
PHOSPHATE ION / BCL-6 corepressor-like protein 1 / Polycomb group RING finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BCL-6 corepressor-like protein 1
B: Polycomb group RING finger protein 1
C: BCL-6 corepressor-like protein 1
D: Polycomb group RING finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5768
Polymers50,1964
Non-polymers3804
Water4,720262
1
A: BCL-6 corepressor-like protein 1
B: Polycomb group RING finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2884
Polymers25,0982
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-26 kcal/mol
Surface area11130 Å2
MethodPISA
2
C: BCL-6 corepressor-like protein 1
D: Polycomb group RING finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2884
Polymers25,0982
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-23 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.784, 65.794, 56.517
Angle α, β, γ (deg.)90.00, 94.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BCL-6 corepressor-like protein 1 / BCoR-L1 / BCoR-like protein 1


Mass: 14023.914 Da / Num. of mol.: 2 / Fragment: UNP residues 1594-1711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCORL1 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5H9F3
#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.: 2 / 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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium citrate, 19% polyethylene glycol (PEG) 1500, 100 mM dibasic sodium phosphate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→19.71 Å / Num. obs: 32631 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4455 / Rsym value: 0.415 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HPL

4hpl


Resolution: 1.85→19.71 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 1994 6.12 %random
Rwork0.1992 ---
obs0.2021 32594 98.69 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 20 262 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063297
X-RAY DIFFRACTIONf_angle_d1.0034461
X-RAY DIFFRACTIONf_dihedral_angle_d14.5091261
X-RAY DIFFRACTIONf_chiral_restr0.066489
X-RAY DIFFRACTIONf_plane_restr0.006571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89620.40371090.3531911X-RAY DIFFRACTION85
1.8962-1.94750.42571420.342162X-RAY DIFFRACTION98
1.9475-2.00470.29271450.24062190X-RAY DIFFRACTION100
2.0047-2.06940.27631320.21052213X-RAY DIFFRACTION100
2.0694-2.14320.2841560.19672169X-RAY DIFFRACTION100
2.1432-2.22890.31531430.21352203X-RAY DIFFRACTION100
2.2289-2.33020.35471440.2272216X-RAY DIFFRACTION100
2.3302-2.45290.2591510.19592202X-RAY DIFFRACTION100
2.4529-2.60620.25681370.19662212X-RAY DIFFRACTION100
2.6062-2.80690.27641460.21072213X-RAY DIFFRACTION100
2.8069-3.08840.25591490.20842218X-RAY DIFFRACTION100
3.0884-3.53310.2061610.18612207X-RAY DIFFRACTION100
3.5331-4.44290.20711340.1632231X-RAY DIFFRACTION100
4.4429-19.710.18721450.18052253X-RAY DIFFRACTION99

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