[English] 日本語
Yorodumi
- PDB-2fi2: Solution structure of the SCAN homodimer from MZF-1/ZNF42 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fi2
TitleSolution structure of the SCAN homodimer from MZF-1/ZNF42
ComponentsZinc finger protein 42
KeywordsTRANSCRIPTION / SCAN domain / Znf-42 / MZF-1 / homodimer / transcription factor / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II ...DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding
Similarity search - Function
DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myeloid zinc finger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Peterson, F.C. / Sander, T.L. / Waltner, J.K. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the SCAN domain from the tumor suppressor protein MZF1.
Authors: Peterson, F.C. / Hayes, P.L. / Waltner, J.K. / Heisner, A.K. / Jensen, D.R. / Sander, T.L. / Volkman, B.F.
History
DepositionDec 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger protein 42
B: Zinc finger protein 42


Theoretical massNumber of molelcules
Total (without water)21,0362
Polymers21,0362
Non-polymers00
Water00
1


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

-
Components

#1: Protein Zinc finger protein 42 / Myeloid zinc finger 1 / MZF-1 / Zinc finger and SCAN domain containing protein 6


Mass: 10517.890 Da / Num. of mol.: 2 / Fragment: SCAN domain, residues 37-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF42, MZF1, ZSCAN6 / Plasmid: pQE30GB1 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: P28698

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
1423D 13C-F1-filtered-13C-F3-separated NOESY
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM ZNF-42 U-15N/13C, 20 mM sodium phosphate, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
21.7 mM ZNF-42 U-15N/13C, 1.7 mM unlabeled ZNF-42, 20 mM sodium phosphate, 50 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 99 mM / pH: 7.4 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.3.SCHWIETERS, C.D., KUSZEWSKI, J.J., TJANDRA, N., CLORE, G.M.refinement
XwinNMR3.5collection
NMRPipe2004processing
SPSCAN1.1.0data analysis
XEASY1.3data analysis
GARANT2.1data analysis
CYANA2.1structure solution
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 4063 NOE CONSTRAINTS ( 843 INTRA, 818 SEQUENTIAL, 1029 MEDIUM, 750 INTRAMONOMER LONG RANGE AND 623 INTERMONOMER NOE CONSTRAINTS) AND 264 PHI AND ...Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 4063 NOE CONSTRAINTS ( 843 INTRA, 818 SEQUENTIAL, 1029 MEDIUM, 750 INTRAMONOMER LONG RANGE AND 623 INTERMONOMER NOE CONSTRAINTS) AND 264 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINTS IN THE SECOND MONOMER. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 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://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