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- PDB-1k91: Solution Structure of Calreticulin P-domain subdomain (residues 2... -

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Basic information

Entry
Database: PDB / ID: 1k91
TitleSolution Structure of Calreticulin P-domain subdomain (residues 221-256)
ComponentsCALRETICULIN
KeywordsMETAL TRANSPORT / HAIRPIN
Function / homology
Function and homology information


response to biphenyl / Scavenging by Class A Receptors / Calnexin/calreticulin cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / response to peptide / cortical granule ...response to biphenyl / Scavenging by Class A Receptors / Calnexin/calreticulin cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / response to peptide / cortical granule / cellular response to electrical stimulus / complement component C1q complex binding / regulation of meiotic nuclear division / negative regulation of retinoic acid receptor signaling pathway / response to glycoside / endoplasmic reticulum quality control compartment / sarcoplasmic reticulum lumen / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / molecular sequestering activity / cortical actin cytoskeleton organization / nuclear androgen receptor binding / cellular response to lithium ion / response to testosterone / protein localization to nucleus / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of cell cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / ERAD pathway / protein export from nucleus / positive regulation of endothelial cell migration / acrosomal vesicle / sarcoplasmic reticulum / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / cellular senescence / unfolded protein binding / integrin binding / protein folding / response to estradiol / nuclear envelope / carbohydrate binding / spermatogenesis / collagen-containing extracellular matrix / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of DNA-templated transcription / mRNA binding / glutamatergic synapse / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsEllgaard, L. / Bettendorff, P. / Braun, D. / Herrmann, T. / Fiorito, F. / Guntert, P. / Helenius, A. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: NMR Structures of 36 and 73-residue Fragments of the Calreticulin P-domain
Authors: Ellgaard, L. / Bettendorff, P. / Braun, D. / Herrmann, T. / Fiorito, F. / Jelesarov, I. / Guntert, P. / Helenius, A. / Wuthrich, K.
History
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / 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 1.4May 22, 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: CALRETICULIN


Theoretical massNumber of molelcules
Total (without water)4,3091
Polymers4,3091
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)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide CALRETICULIN / CRP55 / CALREGULIN / HACBP / ERP60 / CALBP / CALCIUM-BINDING PROTEIN 3 / CABP3


Mass: 4308.620 Da / Num. of mol.: 1 / Fragment: P-DOMAIN, RESIDUES 221-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P18418

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131E-COSY
1412D TOCSY

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Sample preparation

DetailsContents: 5.3 mM CALRETICULIN P-DOMAIN SUBDOMAIN; 25 mM NaCl; 50 mM Sodium Phosphate Buffer;90% H20 10% D2O
Solvent system: 90% H20 10% D2O
Sample conditionsIonic strength: 25 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 280 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
DYANA1.82Guentertstructure solution
DYANA1.82Guentertrefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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