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- PDB-6mf8: TCR alpha transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 6mf8
TitleTCR alpha transmembrane domain
ComponentsT-cell receptor alpha chain C region
KeywordsIMMUNE SYSTEM / mechanoreceptor / transmembrane / TCR
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / response to bacterium / adaptive immune response
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell receptor alpha chain constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBrazin, K.N. / Reinherz, E.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047467 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI100643 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI138489 United States
CitationJournal: Immunity / Year: 2018
Title: The T Cell Antigen Receptor alpha Transmembrane Domain Coordinates Triggering through Regulation of Bilayer Immersion and CD3 Subunit Associations.
Authors: Brazin, K.N. / Mallis, R.J. / Boeszoermenyi, A. / Feng, Y. / Yoshizawa, A. / Reche, P.A. / Kaur, P. / Bi, K. / Hussey, R.E. / Duke-Cohan, J.S. / Song, L. / Wagner, G. / Arthanari, H. / Lang, ...Authors: Brazin, K.N. / Mallis, R.J. / Boeszoermenyi, A. / Feng, Y. / Yoshizawa, A. / Reche, P.A. / Kaur, P. / Bi, K. / Hussey, R.E. / Duke-Cohan, J.S. / Song, L. / Wagner, G. / Arthanari, H. / Lang, M.J. / Reinherz, E.L.
History
DepositionSep 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2May 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: T-cell receptor alpha chain C region


Theoretical massNumber of molelcules
Total (without water)5,2501
Polymers5,2501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, chain is monomeric
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5140 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide T-cell receptor alpha chain C region


Mass: 5250.164 Da / Num. of mol.: 1 / Fragment: Transmembrane domain, residues 93-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcra / Production host: Escherichia coli (E. coli) / References: UniProt: P01849

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
115isotropic12D 1H-15N HSQC
124isotropic23D HNCA
134isotropic23D HN(CA)CB
144isotropic23D HNCO
154isotropic23D HN(CO)CA
163isotropic13D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle50.5 mM [U-99% 15N] TCRa, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
micelle32 mM U-15N; U-2H; Ile, Leu, Val selective labeling TCRa, 90% H2O/10% D2OILV_12C_15N_sample90% H2O/10% D2O
micelle41 mM [U-99% 13C; U-99% 15N] TCRa, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTCRa_HSQC[U-99% 15N]5
2 mMTCRa_NOEU-15N; U-2H; Ile, Leu, Val selective labeling3
1 mMTCRa_backbone[U-99% 13C; U-99% 15N]4
Sample conditionsIonic strength: 30 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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