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- PDB-2kpe: Refined structure of Glycophorin A transmembrane segment dimer in... -

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Basic information

Entry
Database: PDB / ID: 2kpe
TitleRefined structure of Glycophorin A transmembrane segment dimer in DPC micelles
ComponentsGlycophorin-A
KeywordsMEMBRANE PROTEIN / Glycophorin A / transmembrane dimer / micelles / Blood group antigen / Cell membrane / Glycoprotein / Host-virus interaction / Membrane / Sialic acid / Transmembrane
Function / homology
Function and homology information


ankyrin-1 complex / Cell surface interactions at the vascular wall / virus receptor activity / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Glycophorin, conserved site / : / Glycophorin A / Glycophorin A signature. / Glycophorin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsMineev, K.S. / Bocharov, E.V. / Goncharuk, M.V. / Arseniev, A.S. / Volynsky, P.E. / Efremov, R.G.
CitationJournal: Acta Naturae / Year: 2011
Title: Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments.
Authors: Mineev, K.S. / Bocharov, E.V. / Volynsky, P.E. / Goncharuk, M.V. / Tkach, E.N. / Ermolyuk, Y.S. / Schulga, A.A. / Chupin, V.V. / Maslennikov, I.V. / Efremov, R.G. / Arseniev, A.S.
History
DepositionOct 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycophorin-A
B: Glycophorin-A


Theoretical massNumber of molelcules
Total (without water)6,3222
Polymers6,3222
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 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Glycophorin-A / PAS-2 / Sialoglycoprotein alpha / MN sialoglycoprotein


Mass: 3160.857 Da / Num. of mol.: 2 / Fragment: transmembrane segment (UNP residues 89-117)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYPA, GPA / Production host: Escherichia coli (E. coli) / References: UniProt: P02724

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 3 mM [U-100% 13C; U-100% 15N] GpA, 3 mM GpA, 180 mM [U-2H] DPC, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMGpA-1[U-100% 13C; U-100% 15N]1
3 mMGpA-21
180 mMDPC-3[U-2H]1
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: CYANA
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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