- PDB-1znm: A zinc finger with an artificial beta-turn, original sequence tak... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1znm
Title
A zinc finger with an artificial beta-turn, original sequence taken from the third zinc finger domain of the human transcriptional repressor protein YY1 (YING and YANG 1, a delta transcription factor), nmr, 34 structures
response to prostaglandin F / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / RNA localization / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / Ino80 complex / chromatin silencing complex / negative regulation of interferon-beta production ...response to prostaglandin F / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / RNA localization / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / Ino80 complex / chromatin silencing complex / negative regulation of interferon-beta production / response to UV-C / anterior/posterior pattern specification / DNA-binding transcription repressor activity / regulation of chromosome organization / immunoglobulin heavy chain V-D-J recombination / regulation of DNA replication / SMAD binding / regulation of embryonic development / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / regulation of DNA repair / four-way junction DNA binding / positive regulation of DNA repair / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / telomere maintenance / B cell differentiation / negative regulation of miRNA transcription / DNA Damage Recognition in GG-NER / double-strand break repair via homologous recombination / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / cellular response to UV / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function
Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
ROESY
1
2
1
NOESY
1
3
1
COSY
1
4
1
TOCSY
-
Sample preparation
Sample conditions
pH: 6.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AMX
Bruker
AMX
600
1
Varian VXR600
Varian
VXR600
600
2
-
Processing
Software
Name
Version
Classification
X-PLOR
3.851
modelbuilding
X-PLOR
3.851
refinement
X-PLOR
3.851
phasing
NMR software
Name
Developer
Classification
X-PLOR
BRUNGER
refinement
X-PLOR
structuresolution
Refinement
Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING AN AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI AND PSI ANGLES. THE ...Details: THE STRUCTURES WERE CALCULATED USING AN AB-INITIO SIMULATED ANNEALING PROTOCOL ESSENTIALLY AS SUPPLIED WITH X-PLOR 3.851, STARTING FROM STRUCTURES WITH RANDOMIZED PHI AND PSI ANGLES. THE ZINC ION WAS INCORPORATED WITH THE APPROPRIATE GEOMETRIC CONSTRAINTS TO PRODUCE TETRAHEDRAL ZINC CO-ORDINATION.
NMR ensemble
Conformer selection criteria: NO NOE VIOLATIONS ABOVE 0.2 ANGSTROM AND 5 DEGREE DIHEDRAL ANGLE Conformers calculated total number: 100 / Conformers submitted total number: 34
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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