[English] 日本語
Yorodumi
- PDB-7d8a: Crystal Structure of H3(1-13)/PHF14-PZP fusion protein -

+
Open data


ID or keywords:

Loading...

-
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 / Histone H3 signature 1. ...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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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 .

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more