[English] 日本語
Yorodumi
- PDB-1jzu: Cell transformation by the myc oncogene activates expression of a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jzu
TitleCell transformation by the myc oncogene activates expression of a lipocalin: analysis of the gene (Q83) and solution structure of its protein product
Componentslipocalin Q83
KeywordsLIPID BINDING PROTEIN / BETA BARREL / LIPOCALIN
Function / homology
Function and homology information


oleic acid binding / enterobactin binding / arachidonate binding / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Extracellular fatty acid-binding protein
Similarity search - Component
Biological speciesCoturnix coturnix (Common quail)
MethodSOLUTION NMR / ARIA, CNS automated refinement using also ambiguous NOE distance constraints; simulated annealing (torsion angle dynamics)
AuthorsHartl, M. / Matt, T. / Schueler, W. / Siemeister, G. / Kontaxis, G. / Kloiber, K. / Konrat, R. / Bister, K.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Cell Transformation by the v-myc Oncogene Abrogates c-Myc/Max-mediated Suppression of a C/EBPbeta-dependent Lipocalin Gene.
Authors: Hartl, M. / Matt, T. / Schueler, W. / Siemeister, G. / Kontaxis, G. / Kloiber, K. / Konrat, R. / Bister, K.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: Sequence-Specific Resonance Assignments of Q83, a Lipocalin Highly Expressed in v-myc-Transformed Avian Fibroblasts
Authors: Kontaxis, G. / Matt, T. / Schueler, W. / Kraeutler, B. / Bister, K. / Konrat, R.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: lipocalin Q83


Theoretical massNumber of molelcules
Total (without water)18,1051
Polymers18,1051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #15closest to the average

-
Components

#1: Protein lipocalin Q83


Mass: 18104.734 Da / Num. of mol.: 1 / Mutation: A1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix coturnix (Common quail) / Plasmid: pET3d-Q83 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9I9P7
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-TOCSY
1213D CCH-TOCSY-NNH
1313D NOESY-HSQC:(two 13C,Ca/methyl-centered,15N)
1413D HNHA
151Cross-correlated relaxation rates Ca(i)Ha(i)-DD/C'(i)-CSA
161Cross-correlated relaxation rates Ca(i)Ha(i)-DD/C'(i-1)-CSA

-
Sample preparation

DetailsContents: 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol
pH: 6.4 / Pressure: ambient / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 Rev BVarian Associates, Inc.collection
NMRPipe1.8 Rev 2001.030.21.27Delaglioprocessing
ANSIG3.3Kraulisdata analysis
NMRView4.1.3Johnson (Merck and Co., Inc.)data analysis
ARIA/CNS1Linge, Nilges, Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: ARIA, CNS automated refinement using also ambiguous NOE distance constraints; simulated annealing (torsion angle dynamics)
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
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