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- PDB-8hcu: Crystal structure of BCOR/PCGF1/KDM2B complex -

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Basic information

Entry
Database: PDB / ID: 8hcu
TitleCrystal structure of BCOR/PCGF1/KDM2B complex
Components
  • BCL-6 corepressor
  • Polycomb group RING finger protein 1
  • cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B
KeywordsTRANSCRIPTION / complex / PRC1
Function / homology
Function and homology information


negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / negative regulation of bone mineralization / unmethylated CpG binding / PcG protein complex / blastocyst hatching / odontogenesis / roof of mouth development ...negative regulation of tooth mineralization / BCOR complex / specification of axis polarity / PRC1 complex / negative regulation of bone mineralization / unmethylated CpG binding / PcG protein complex / blastocyst hatching / odontogenesis / roof of mouth development / histone demethylase activity / heat shock protein binding / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin 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 / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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 / PHD-finger / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / : ...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 / PHD-finger / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / : / Zinc finger, C3HC4 type (RING finger) / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Ankyrin repeat-containing domain superfamily / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ACETIC ACID / cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B / BCL-6 corepressor / Polycomb group RING finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsShen, F. / Chen, R. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504104 China
CitationJournal: Commun Biol / Year: 2024
Title: Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation.
Authors: Chen, R. / Shen, F. / Zhang, Y. / Sun, M. / Dong, Y. / Yin, Y. / Su, C. / Peng, C. / Liu, J. / Xu, J.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B
B: Polycomb group RING finger protein 1
C: BCL-6 corepressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3235
Polymers55,2033
Non-polymers1202
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.291, 67.291, 252.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B


Mass: 26469.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4DSN4
#2: Protein Polycomb group RING finger protein 1 / Nervous system Polycomb-1 / NSPc1 / RING finger protein 68


Mass: 12636.700 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCGF1, NSPC1, RNF68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BSM1
#3: Protein BCL-6 corepressor / BCoR


Mass: 16096.708 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCOR, KIAA1575 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6W2J9
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.4 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 0.1M magnesium acetate, 0.1M sodium citrate pH6.2, 4% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→126.02 Å / Num. obs: 30637 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Rrim(I) all: 0.122 / Χ2: 1.02 / Net I/σ(I): 12 / Num. measured all: 421860
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 99.9 % / Redundancy: 14.6 % / Rmerge(I) obs: 1.218 / Num. measured all: 37997 / Num. unique obs: 2605 / CC1/2: 0.936 / Rpim(I) all: 0.329 / Rrim(I) all: 1.262 / Χ2: 1.04 / Net I/σ(I) obs: 2.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JH5, 4HPL

5jh5

4hpl


Resolution: 2.2→65.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 15.499 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1522 5 %RANDOM
Rwork0.20023 ---
obs0.20214 29020 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.831 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--2.79 Å20 Å2
3----5.58 Å2
Refinement stepCycle: 1 / Resolution: 2.2→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 8 62 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163500
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6444864
X-RAY DIFFRACTIONr_angle_other_deg0.3821.5758053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.533529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31410663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
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_it2.6014.4231749
X-RAY DIFFRACTIONr_mcbond_other2.5894.4191747
X-RAY DIFFRACTIONr_mcangle_it3.8457.9332175
X-RAY DIFFRACTIONr_mcangle_other3.8477.9352176
X-RAY DIFFRACTIONr_scbond_it3.5344.8951845
X-RAY DIFFRACTIONr_scbond_other3.5334.8961846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5118.8182690
X-RAY DIFFRACTIONr_long_range_B_refined7.17543.233850
X-RAY DIFFRACTIONr_long_range_B_other7.17743.243851
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 124 -
Rwork0.308 2104 -
obs--99.91 %
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)
13.380.7420.23431.5265-0.16733.8181-0.03230.08980.05720.02380.0137-0.1406-0.06920.58960.01860.0242-0.0133-0.00190.1014-0.01170.035426.76481.651513.2679
23.5216-0.6471-0.1265.49550.5786.63810.02470.29520.3379-0.39340.01470.0068-0.6583-0.2207-0.03940.1425-0.03910.04120.1137-0.03810.0946-7.7802-33.723720.7636
31.3396-1.58220.55264.1705-0.53693.4686-0.0873-0.08960.05940.19870.12480.0044-0.0859-0.2232-0.03750.0421-0.0410.03870.1061-0.04540.0883-0.9816-51.637216.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1102 - 1335
2X-RAY DIFFRACTION2B162 - 254
3X-RAY DIFFRACTION3C1619 - 1746

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