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- PDB-2mti: NMR structure of the lymphocyte receptor NKR-P1A -

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Basic information

Entry
Database: PDB / ID: 2mti
TitleNMR structure of the lymphocyte receptor NKR-P1A
ComponentsKiller cell lectin-like receptor subfamily B member 1A
KeywordsIMMUNE SYSTEM / C-type lectin-like domain / NK cells / NK receptor / NKR-P1A
Function / homology
Function and homology information


Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Killer cell lectin-like receptor subfamily B member 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChmelik, J. / Rozbesky, D. / Pospisilova, E. / Adamek, D. / Novak, P.
CitationJournal: Proteins / Year: 2016
Title: Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structure.
Authors: Rozbesky, D. / Adamek, D. / Pospisilova, E. / Novak, P. / Chmelik, J.
History
DepositionAug 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Killer cell lectin-like receptor subfamily B member 1A


Theoretical massNumber of molelcules
Total (without water)16,0091
Polymers16,0091
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Killer cell lectin-like receptor subfamily B member 1A


Mass: 16008.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Klrb1a / Production host: Escherichia coli (E. coli) / References: UniProt: G5E882

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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 aliphatic
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1813D HN(CA)CO
1913D H(CCO)NH
11013D H(CCO)NH
11113D (H)CCH-TOCSY aliphatic
11213D 1H-15N NOESY
11312D 1H-13C HSQC aromatic
11413D (H)CCH-TOCSY aromatic
11512D (HB)CB(CGCD)HD
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] NKR-P1A, 15 mM PIPES, 50 mM sodium chloride, 1 mM sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNKR-P1A-1[U-100% 13C; U-100% 15N]1
15 mMPIPES-21
50 mMsodium chloride-31
1 mMsodium azide-41
90 %H2O-51
10 %D2O-61
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.3.6Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RECOORDBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CING(CING) Vuister, Doreleijer, da Silvavalidation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2453 / NOE intraresidue total count: 1124 / NOE long range total count: 628 / NOE medium range total count: 216 / NOE sequential total count: 485 / Hydrogen bond constraints total count: 60 / Protein chi angle constraints total count: 55 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.5 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.015394498 Å / Distance rms dev error: 0.0009642876 Å

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