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- PDB-6l7z: Solution NMR structure of the N-terminal immunoglobulin variable ... -

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Basic information

Entry
Database: PDB / ID: 6l7z
TitleSolution NMR structure of the N-terminal immunoglobulin variable domain of BTNL2
ComponentsButyrophilin-like protein 2
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / T cell co-inhibitory molecule
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / negative regulation of T cell receptor signaling pathway / regulation of cytokine production / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / T cell receptor signaling pathway / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Butyrophilin-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBasak, A.J. / Lee, W. / Samanta, D. / De, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)ECR/2016/000847 India
Department of Science & Technology (DST, India)ECR/2016/000923 India
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Insights into N-terminal IgV Domain of BTNL2, a T Cell Inhibitory Molecule, Suggests a Non-canonical Binding Interface for Its Putative Receptors.
Authors: Basak, A.J. / Maiti, S. / Hansda, A. / Mahata, D. / Duraivelan, K. / Kundapura, S.V. / Lee, W. / Mukherjee, G. / De, S. / Samanta, D.
History
DepositionNov 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin-like protein 2


Theoretical massNumber of molelcules
Total (without water)13,3401
Polymers13,3401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Butyrophilin-like protein 2


Mass: 13340.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Btnl2, Gm315, Ng9 / Production host: Escherichia coli (E. coli) / References: UniProt: O70355

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
222isotropic12D 1H-13C HSQC aliphatic
232isotropic13D CBCA(CO)NH
242isotropic13D HN(CA)CB
252isotropic13D HNCO
262isotropic13D (H)CCH-TOCSY
272isotropic13D HBHA(CO)NH
181isotropic12D 1H-1H NOESY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-15N TOCSY
2112isotropic13D 1H-13C NOESY
2122isotropic13D HN(CA)CO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-99% 15N] BTNL2, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O15N_sample93% H2O/7% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] BTNL2, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O15N_13C_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMBTNL2[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.4 mMBTNL2[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
190 mMconditions_16.5 1 atm298 K
290 mMconditions_26.5 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: Cryoprobe equipped

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
PONDEROSA-C/SLee W, Petit CM, Cornilescu G, Stark JL, Markley JLstructure calculation
PONDEROSA-C/SLee W, Petit CM, Cornilescu G, Stark JL, Markley JLrefinement
PyMOLThe PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC.refinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JLrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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