[English] 日本語
Yorodumi
- PDB-2mma: NMR-based docking model of GrxS14-BolA2 apo-heterodimer from Arab... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mma
TitleNMR-based docking model of GrxS14-BolA2 apo-heterodimer from Arabidopsis thaliana
Components
  • BolA2
  • Monothiol glutaredoxin-S14, chloroplastic
KeywordsGENE REGULATION / stress-responsive protein / transcriptional regulator
Function / homology
Function and homology information


chloroplast envelope / response to iron ion / antiporter activity / chloroplast stroma / monoatomic cation transport / protein maturation / chloroplast / 2 iron, 2 sulfur cluster binding / response to oxidative stress / intracellular iron ion homeostasis ...chloroplast envelope / response to iron ion / antiporter activity / chloroplast stroma / monoatomic cation transport / protein maturation / chloroplast / 2 iron, 2 sulfur cluster binding / response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BolA-like protein 2 / Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. ...BolA-like protein 2 / Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / GMP Synthetase; Chain A, domain 3 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Monothiol glutaredoxin-S14, chloroplastic / Protein BOLA2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / molecular dynamics, energy minimization
Model detailslowest energy, model1
AuthorsRoret, T. / Tsan, P. / Couturier, J. / Rouhier, N. / Didierjean, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Spectroscopic Insights into BolA-Glutaredoxin Complexes.
Authors: Roret, T. / Tsan, P. / Couturier, J. / Zhang, B. / Johnson, M.K. / Rouhier, N. / Didierjean, C.
History
DepositionMar 13, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monothiol glutaredoxin-S14, chloroplastic
B: BolA2


Theoretical massNumber of molelcules
Total (without water)22,6132
Polymers22,6132
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)1 / 1all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein Monothiol glutaredoxin-S14, chloroplastic / AtGRXcp / AtGrxS14 / CAX-interacting protein 1 / CXIP1


Mass: 12354.149 Da / Num. of mol.: 1 / Fragment: UNP residues 67-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GRXS14, CXIP1, At3g54900, F28P10.120 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q84Y95
#2: Protein BolA2 / BolA-like family protein


Mass: 10258.644 Da / Num. of mol.: 1 / Fragment: UNP residues 2-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT5G09830, At5g09830 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIC3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.12 mM [U-100% 15N] BolA2, 0.012-0.24 mM GrxS14, 90% H2O/10% D2O90% H2O/10% D2O
20.12 mM [U-100% 15N] GrxS14, 0.012-0.24 mM BolA2, 90% H2O/10% D2O90% H2O/10% D2O
30.12 mM [U-100% 15N] GrxS14, 90% H2O/10% D2O90% H2O/10% D2O
40.12 mM [U-100% 15N] BolA2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.12 mMBolA2-1[U-100% 15N]1
mMGrxS14-20.012-0.241
0.12 mMGrxS14-3[U-100% 15N]2
mMBolA2-40.012-0.242
0.12 mMGrxS14-5[U-100% 15N]3
0.12 mMBolA2-6[U-100% 15N]4
Sample conditionsIonic strength: 0.05 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
GRAMM-X_Protein-Protein_Docking_Web_Server1.2.0Tovchigrechkostructure solution
YASARA_Energy_Minimization_ServerKriegergeometry optimization
YASARA_Energy_Minimization_ServerKriegerrefinement
GRAMM-X_Protein-Protein_Docking_Web_ServerTovchigrechkorefinement
RefinementMethod: molecular dynamics, energy minimization / Software ordinal: 1
Details: Energy minimization using the YASARA force field. The structure was moved to a nearby (local) minimum, with removal of clashes and small errors.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 1 / Conformers submitted total number: 1

+
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