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- PDB-7d8a: Crystal Structure of H3(1-13)/PHF14-PZP fusion protein -

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Basic information

Entry
Database: PDB / ID: 7d8a
TitleCrystal Structure of H3(1-13)/PHF14-PZP fusion protein
Components
  • Gene for histone H3 (germline gene)
  • PHD finger protein 14
KeywordsGENE REGULATION / H3(1-13)/PHF14-PZP
Function / homology
Function and homology information


negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / structural constituent of chromatin / nucleosome / histone binding ...negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / structural constituent of chromatin / nucleosome / histone binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
: / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...: / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / 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 / Histone H3 signature 1. / Histone H3/CENP-A / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 14 / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14.
Authors: Zheng, S. / Bi, Y. / Chen, H. / Gong, B. / Jia, S. / Li, H.
History
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 14
E: Gene for histone H3 (germline gene)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4109
Polymers25,0032
Non-polymers4077
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-19 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.781, 150.423, 81.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

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Components

#1: Protein PHD finger protein 14


Mass: 23262.160 Da / Num. of mol.: 1 / Fragment: PHF14-PZP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: phf14 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A286Y9D1
#2: Protein/peptide Gene for histone H3 (germline gene)


Mass: 1740.877 Da / Num. of mol.: 1 / Fragment: H3(1-13)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: V9H1G0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 18% PEG4000, 12% isopropanol .

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2818 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 33740 / % possible obs: 93.9 % / Redundancy: 13.2 % / Rsym value: 0.125 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1282 / Rsym value: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D86

7d86


Resolution: 2→40.71 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.53 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 3170 10.09 %
Rwork0.1774 28234 -
obs0.181 31404 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.39 Å2 / Biso mean: 48.24 Å2 / Biso min: 15.82 Å2
Refinement stepCycle: final / Resolution: 2→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 7 115 1737
Biso mean--34.52 42.37 -
Num. residues----210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.28091150.243213041419100
2.03-2.050.26331230.2527901102498
2.1-2.130.28961320.213112371369100
2.13-2.170.2691390.201513141453100
2.17-2.210.25481410.19641318145999
2.21-2.260.24611590.186512761435100
2.26-2.310.24681650.199212951460100
2.31-2.360.26211320.196213231455100
2.36-2.420.25191430.195713091452100
2.42-2.480.22281240.18731306143099
2.48-2.560.22721480.18861306145499
2.56-2.640.20311580.185913031461100
2.64-2.730.26721390.190913091448100
2.73-2.840.24721430.199313201463100
2.84-2.970.23281560.180413211477100
2.97-3.130.23921610.180412861447100
3.13-3.320.18231430.168812901433100
3.33-3.580.21131600.16831304146499
3.58-3.940.18241440.14761278142299
3.94-4.510.15581630.147413141477100
4.51-5.680.18561660.164212771443100
5.68-40.710.21031160.18341343145999
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)
12.02150.50480.04623.1011-0.45931.22220.10330.01980.7745-0.5152-0.06590.0151-0.61550.0210.01260.42010.03450.03630.1295-0.03050.4084-17.6804-13.2589-1.5069
23.65640.0254-0.75091.9150.48722.22460.0519-0.21280.3841-0.0731-0.0602-0.064-0.19350.02510.04350.19930.0097-0.01450.203-0.01420.1854-13.3597-29.78634.2351
32.47530.77310.23952.20980.89783.4983-0.02220.73810.1272-1.2892-0.2216-0.22280.3909-0.33460.05141.10240.1630.05510.45660.18380.454-14.0002-5.1386-14.7961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 285 through 377 )A285 - 377
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 485 )A378 - 485
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 9 )E1 - 9

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