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- PDB-7d87: Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) -

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Basic information

Entry
Database: PDB / ID: 7d87
TitleCrystal Structure of zebrafish PHF14-PZP in complex with H3(1-25)
Components
  • Gene for histone H3 (germline gene)
  • PHD finger protein 14
KeywordsGENE REGULATION / 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: 2.11 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)26,3919
Polymers25,9832
Non-polymers4077
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-21 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.921, 151.019, 81.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PHD finger protein 14


Mass: 23349.238 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: 2634.090 Da / Num. of mol.: 1 / Fragment: histone H3(1-25) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / 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.: 87 / 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: 2.49 Å3/Da / Density % sol: 50.65 % / Mosaicity: 0.391 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15363 / % possible obs: 99.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Χ2: 1.524 / Net I/σ(I): 7 / Num. measured all: 181303
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.148.70.8897480.8540.3060.9430.5799.9
2.14-2.189.60.8077630.8560.2680.8510.58999.9
2.18-2.2210.30.77550.9140.2240.7360.626100
2.22-2.2610.90.687410.9180.2120.7130.63199.9
2.26-2.3111.60.6047680.9560.1840.6320.6599.7
2.31-2.3711.80.5677390.9480.1710.5930.657100
2.37-2.4212.30.5197560.9650.1530.5420.683100
2.42-2.4912.40.4397730.9710.1290.4580.731100
2.49-2.5612.20.3967520.9770.1180.4140.793100
2.56-2.6511.30.3337570.9720.1040.350.81599.7
2.65-2.7412.90.2657630.9830.0770.2760.896100
2.74-2.8513.40.2437550.9870.0680.2521.10299.7
2.85-2.9813.40.1957800.9920.0550.2021.23399.7
2.98-3.1413.20.1547540.9950.0440.161.70599.7
3.14-3.3312.90.1347690.9940.0390.142.083100
3.33-3.5912.20.1087750.9960.0320.1132.631100
3.59-3.9511.10.097770.9960.0280.0952.98999.5
3.95-4.5212.80.0797960.9980.0230.0823.262100
4.52-5.712.30.0727920.9980.0210.0753.29799.9
5.7-5010.70.0618500.9980.0190.0643.55698.8

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Processing

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

7d86


Resolution: 2.11→32.21 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 765 4.99 %
Rwork0.1651 14575 -
obs0.167 15340 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.4 Å2 / Biso mean: 58.8207 Å2 / Biso min: 21.58 Å2
Refinement stepCycle: final / Resolution: 2.11→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 7 87 1719
Biso mean--42.58 46.54 -
Num. residues----211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.270.22671460.20362800294698
2.27-2.50.25971450.191828943039100
2.5-2.860.2411670.187328823049100
2.86-3.60.20581510.169829353086100
3.61-32.210.17811560.145930643220100
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)
12.1688-0.29380.2324.3283-0.61431.52710.1083-0.0902-0.64920.5834-0.0089-0.01620.5843-0.0096-0.0560.4894-0.04-0.02380.2374-0.0360.44252.770214.42011.6444
24.15280.24450.55811.99860.00811.89070.01050.2823-0.3531-0.0086-0.0206-0.11880.1081-0.0203-0.00050.19870.0050.01320.2397-0.04120.19268.508830.1517-4.986
31.17970.19990.44210.95910.94021.0204-0.197-0.67970.29711.2355-0.0682-0.229-0.3458-0.62860.08721.2135-0.0994-0.07160.63290.10960.6676.75395.336414.8804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 284 through 387 )A284 - 387
2X-RAY DIFFRACTION2chain 'A' and (resid 388 through 485 )A388 - 485
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 9 )E1 - 9

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