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- PDB-7cmz: Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 -

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Basic information

Entry
Database: PDB / ID: 7cmz
TitleCrystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8
Components
  • DNA topoisomerase 2-binding protein 1
  • Histone lysine demethylase PHF8
KeywordsPROTEIN BINDING/HYDROLASE / TOPBP1 / PROTEIN BINDING-HYDROLASE complex
Function / homology
Function and homology information


broken chromosome clustering / histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / BRCA1-B complex / negative regulation of rDNA heterochromatin formation / phosphorylation-dependent protein binding ...broken chromosome clustering / histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / BRCA1-B complex / negative regulation of rDNA heterochromatin formation / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / histone H3K36 demethylase activity / protein localization to site of double-strand break / DNA replication checkpoint signaling / 2-oxoglutarate-dependent dioxygenase activity / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / response to ionizing radiation / positive regulation of transcription by RNA polymerase I / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / histone H3K9 demethylase activity / Presynaptic phase of homologous DNA pairing and strand exchange / chromosome organization / histone demethylase activity / DNA replication initiation / methylated histone binding / protein serine/threonine kinase activator activity / Condensation of Prophase Chromosomes / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / transcription coregulator activity / double-strand break repair via homologous recombination / brain development / G2/M DNA damage checkpoint / HDMs demethylate histones / G1/S transition of mitotic cell cycle / PML body / spindle pole / actin cytoskeleton / site of double-strand break / chromosome / Processing of DNA double-strand break ends / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / nuclear body / iron ion binding / DNA repair / centrosome / DNA damage response / chromatin binding / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / Jumonji, helical domain / twin BRCT domain / Jumonji helical domain / BRCA1 C Terminus (BRCT) domain / JmjC domain, hydroxylase / breast cancer carboxy-terminal domain ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / Jumonji, helical domain / twin BRCT domain / Jumonji helical domain / BRCA1 C Terminus (BRCT) domain / JmjC domain, hydroxylase / breast cancer carboxy-terminal domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type
Similarity search - Domain/homology
: / DNA topoisomerase 2-binding protein 1 / Histone lysine demethylase PHF8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsChe, S.Y. / Ma, S. / Cao, C. / Yao, Z. / Shi, L. / Yang, N.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81972660 China
National Natural Science Foundation of China (NSFC)31671474 China
Ministry of Science and Technology (MoST, China)2018YFA0107004 China
Ministry of Science and Technology (MoST, China)2019YFA0508902 China
CitationJournal: Sci Adv / Year: 2021
Title: PHF8-promoted TOPBP1 demethylation drives ATR activation and preserves genome stability.
Authors: Ma, S. / Cao, C. / Che, S. / Wang, Y. / Su, D. / Liu, S. / Gong, W. / Liu, L. / Sun, J. / Zhao, J. / Wang, Q. / Song, N. / Ge, T. / Guo, Q. / Tian, S. / Chen, C.D. / Zhang, T. / Wang, J. / ...Authors: Ma, S. / Cao, C. / Che, S. / Wang, Y. / Su, D. / Liu, S. / Gong, W. / Liu, L. / Sun, J. / Zhao, J. / Wang, Q. / Song, N. / Ge, T. / Guo, Q. / Tian, S. / Chen, C.D. / Zhang, T. / Wang, J. / Ding, X. / Yang, F. / Ying, G. / Yang, J. / Zhang, K. / Zhu, Y. / Yao, Z. / Yang, N. / Shi, L.
History
DepositionJul 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2-binding protein 1
B: Histone lysine demethylase PHF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5444
Polymers28,4822
Non-polymers622
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-18 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.517, 60.350, 66.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA topoisomerase 2-binding protein 1 / DNA topoisomerase II-beta-binding protein 1 / TopBP1 / DNA topoisomerase II-binding protein 1


Mass: 26059.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92547
#2: Protein/peptide Histone lysine demethylase PHF8 / PHD finger protein 8 / [histone H3]-dimethyl-L-lysine(36) demethylase PHF8 / [histone H3]-dimethyl- ...PHD finger protein 8 / [histone H3]-dimethyl-L-lysine(36) demethylase PHF8 / [histone H3]-dimethyl-L-lysine(9) demethylase PHF8


Mass: 2422.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UPP1, [histone H3]-dimethyl-L-lysine36 demethylase, [histone H3]-dimethyl-L-lysine9 demethylase
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 31, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.695→40 Å / Num. obs: 24740 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 0.958 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.695-1.736.20.37511980.9290.1620.4090.85299.9
1.73-1.766.40.34212120.9460.1450.3720.83899.9
1.76-1.796.50.29312100.9490.1240.3190.904100
1.79-1.836.40.25812410.9690.110.2810.90699.9
1.83-1.876.40.21212090.9750.090.2310.93399.9
1.87-1.916.10.19512030.9760.0850.2130.98499.6
1.91-1.9660.16412230.9780.0720.181.073100
1.96-2.026.70.13512320.9880.0560.1471.10299.9
2.02-2.076.70.1212280.990.050.131.109100
2.07-2.146.60.10312290.9920.0430.1121.09599.8
2.14-2.226.50.09412100.9930.040.1031.104100
2.22-2.316.20.08712270.9930.0380.0951.05399.8
2.31-2.416.20.07612320.9940.0330.0831.04599.8
2.41-2.546.70.06712330.9960.0280.0730.98399.9
2.54-2.76.60.06112480.9970.0260.0670.892100
2.7-2.916.50.05512510.9970.0230.0590.89699.7
2.91-3.26.20.0512460.9970.0220.0550.89499.8
3.2-3.666.70.04612550.9980.0190.050.90499.9
3.66-4.616.10.04412870.9970.020.0490.90799.8
4.61-406.10.04113660.9980.0170.0440.68899.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3al2

3al2


Resolution: 1.695→34.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.231 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1223 5 %RANDOM
Rwork0.1782 ---
obs0.18 23251 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.52 Å2 / Biso mean: 14.848 Å2 / Biso min: 4.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2---0.03 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.695→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 2 289 2144
Biso mean--18.24 27.01 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131925
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171766
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6322612
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5714105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.99522.212104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7921512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
LS refinement shellResolution: 1.695→1.739 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.249 84 -
Rwork0.231 1473 -
obs--87.28 %

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