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- PDB-2alb: NMR structure of the N-terminal domain a of the glycoprotein chap... -

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Basic information

Entry
Database: PDB / ID: 2alb
TitleNMR structure of the N-terminal domain a of the glycoprotein chaperone ERp57
ComponentsProtein disulfide-isomerase A3
KeywordsISOMERASE / Thioredoxin fold
Function / homology
Function and homology information


Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / protein-disulfide reductase activity ...Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / phospholipase C activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / protein-disulfide reductase activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / platelet aggregation / recycling endosome membrane / melanosome / protein folding / ER-Phagosome pathway / adaptive immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / focal adhesion / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / 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 A3
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsSilvennoinen, L. / Tossavainen, H. / Myllyharju, J. / Permi, P.
CitationJournal: To be Published
Title: NMR structure of the N-terminal domain a of the glycoprotein chaperone ERp57
Authors: Silvennoinen, L. / Tossavainen, H. / Myllyharju, J. / Permi, P.
History
DepositionAug 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)12,0831
Polymers12,0831
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 / 30structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein disulfide-isomerase A3 / Disulfide isomerase ER-60 / ERp60 / 58 kDa microsomal protein / p58 / ERp57 / 58 kDa glucose regulated protein


Mass: 12082.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P30101, protein disulfide-isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 0.8-2.5 mM / pH: 6.3 / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Associates Inc.processing
Sparky3.11Koddard and Knellerdata analysis
CYANA2Guentertstructure solution
Amber8Caserefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 30 / Conformers submitted total number: 20

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