[English] 日本語
Yorodumi
- PDB-2l9z: Zinc knuckle in PRDM4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l9z
TitleZinc knuckle in PRDM4
ComponentsPR domain zinc finger protein 4
KeywordsTRANSCRIPTION / zinc-binding domain
Function / homology
Function and homology information


p75NTR negatively regulates cell cycle via SC1 / histone methyltransferase binding / histone methyltransferase complex / cell fate commitment / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / sequence-specific double-stranded DNA binding / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II ...p75NTR negatively regulates cell cycle via SC1 / histone methyltransferase binding / histone methyltransferase complex / cell fate commitment / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / sequence-specific double-stranded DNA binding / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytoplasm
Similarity search - Function
PR-domain zinc finger protein PRDM4 / PRDM4, zinc knuckle motif / PRDM4, PR/SET domain / PR zinc knuckle motif / PR domain zinc finger protein 2, PR domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger ...PR-domain zinc finger protein PRDM4 / PRDM4, zinc knuckle motif / PRDM4, PR/SET domain / PR zinc knuckle motif / PR domain zinc finger protein 2, PR domain / SET domain superfamily / SET domain profile. / SET domain / 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
Similarity search - Domain/homology
PR domain zinc finger protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsBriknarova, K. / Atwater, D.Z. / Glicken, J.M. / Maynard, S.J. / Ness, T.E.
CitationJournal: Proteins / Year: 2011
Title: The PR/SET domain in PRDM4 is preceded by a zinc knuckle.
Authors: Briknarova, K. / Atwater, D.Z. / Glicken, J.M. / Maynard, S.J. / Ness, T.E.
History
DepositionFeb 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: PR domain zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3822
Polymers4,3171
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide PR domain zinc finger protein 4 / PR domain-containing protein 4


Mass: 4316.885 Da / Num. of mol.: 1 / Fragment: sequence database residues 366-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM4, PFM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9UKN5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
142ECOSY
1532D 1H-15N HSQC
1633D HNHA
1733D HNHB
1833D 1H-15N TOCSY
1933D 1H-15N NOESY
11032D 1H-15N HMQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM PRDM4(366-402), 2.5 mM ZINC ION, 50 mM D11-Tris, 2.5 mM D16-TCEP, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM PRDM4(366-402), 2.5 mM ZINC ION, 50 mM D11-Tris, 2.5 mM D16-TCEP, 100% D2O100% D2O
30.25 mM [U-100% 15N] PRDM4(366-402), 1.6 mM ZINC ION, 50 mM D11-Tris, 2.5 mM D16-TCEP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPRDM4(366-402)-11
2.5 mMZINC ION-21
0.5 mMPRDM4(366-402)-32
2.5 mMZINC ION-42
0.25 mMPRDM4(366-402)-5[U-100% 15N]3
1.6 mMZINC ION-63
Sample conditionsIonic strength: 0 / pH: 7.1-7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
FelixFelix NMR Inc.processing
FelixFelix NMR Inc.chemical shift assignment
FelixFelix NMR Inc.data analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 9 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 14 / Protein psi angle constraints total count: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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