[English] 日本語
Yorodumi
- PDB-2ghf: Solution structure of the complete zinc-finger region of human zi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ghf
TitleSolution structure of the complete zinc-finger region of human zinc-fingers and homeoboxes 1 (ZHX1)
ComponentsZinc fingers and homeoboxes protein 1
KeywordsTRANSCRIPTION / METAL BINDING PROTEIN / C2H2 zinc fingers / 4-stranded parallel/anti-parallel beta-sheet / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm ...cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Homez, homeobox domain / ZHX, C2H2 finger domain / Homeodomain leucine-zipper encoding, Homez / Zinc-fingers and homeoboxes C2H2 finger domain / Classic Zinc Finger / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Double Stranded RNA Binding Domain ...Homez, homeobox domain / ZHX, C2H2 finger domain / Homeodomain leucine-zipper encoding, Homez / Zinc-fingers and homeoboxes C2H2 finger domain / Classic Zinc Finger / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / Homeobox-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc fingers and homeoboxes protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Sparky ASSIGNMENT - CYANA structure calculations; run1: use 70% most intense peaks for initial fold, run2: refine initial fold using all peaks - water refinement with CNS
AuthorsWienk, H. / Structural Proteomics in Europe (SPINE)
CitationJournal: To be Published
Title: Solution structure of the zinc-finger region of human zinc-fingers and homeoboxes 1 (ZHX1)
Authors: Wienk, H. / Lammers, I. / Wu, J. / Hotze, A. / Wechselberger, R. / Kaptein, R. / Folkers, G.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc fingers and homeoboxes protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2643
Polymers12,1341
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with acceptable covalent geometry,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Zinc fingers and homeoboxes protein 1 / ZHX1


Mass: 12133.544 Da / Num. of mol.: 1 / Fragment: zinc-finger region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZHX1 / Plasmid: pDEST-14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (Novagen) / References: UniProt: Q9UKY1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY

-
Sample preparation

DetailsContents: 0.3 mM ZHX1-ZNF; 50 mM NaPO4; 150 mM NaCl; 40 uM ZnCl2, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 8.0 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
XwinNMR3.5BRUKERprocessing
Sparky3Goddard and Knellerdata analysis
CYANA2.1Guntertstructure solution
CNS1.1Brungerrefinement
RefinementMethod: Sparky ASSIGNMENT - CYANA structure calculations; run1: use 70% most intense peaks for initial fold, run2: refine initial fold using all peaks - water refinement with CNS
Software ordinal: 1
Details: Structures are based on 2034 distance restraints (including for each of the two zinc-fingers 4 C2H2-to-Zinc restraints and 6 C2H2 restraints to arrange their Zn-coordinating atoms in a ...Details: Structures are based on 2034 distance restraints (including for each of the two zinc-fingers 4 C2H2-to-Zinc restraints and 6 C2H2 restraints to arrange their Zn-coordinating atoms in a tetrahedron). In addition 192 dihedral restraints were used (100 from TALOS and 92 from CSI).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://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