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- PDB-2dj2: The solution structure of the second thioredoxin domain of mouse ... -

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Basic information

Entry
Database: PDB / ID: 2dj2
TitleThe solution structure of the second thioredoxin domain of mouse Protein disulfide-isomerase A4
ComponentsProtein disulfide-isomerase A4
KeywordsISOMERASE / Protein ERp-72 / ERp72 / Cai / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of protein folding / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / blood coagulation, fibrin clot formation / protein disulfide isomerase activity / smooth endoplasmic reticulum / protein-disulfide reductase activity / chaperone-mediated protein folding / response to endoplasmic reticulum stress / platelet aggregation ...positive regulation of protein folding / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / blood coagulation, fibrin clot formation / protein disulfide isomerase activity / smooth endoplasmic reticulum / protein-disulfide reductase activity / chaperone-mediated protein folding / response to endoplasmic reticulum stress / platelet aggregation / melanosome / integrin binding / protein folding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum / extracellular space
Similarity search - Function
Protein disulphide-isomerase A4 / Protein disulfide-isomerase A4, TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Protein disulphide-isomerase A4 / Protein disulfide-isomerase A4, TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase A4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The solution structure of the second thioredoxin domain of mouse Protein disulfide-isomerase A4
Authors: Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A4


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water0
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,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein disulfide-isomerase A4 / Protein ERp-72 / ERp72


Mass: 13152.770 Da / Num. of mol.: 1 / Fragment: 2nd thioredoxin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Pdia4, Cai, Erp72 / Plasmid: P050425-14 / Production host: Cell free synthesis / References: UniProt: P08003, protein disulfide-isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.2mM Thioredoxin domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.955Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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