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- PDB-7rno: Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated do... -

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Basic information

Entry
Database: PDB / ID: 7rno
TitleModel of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated docking, NMR and restrained MD
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TAP binding protein-like variant
KeywordsIMMUNE SYSTEM / TAPBPR / MR1 / MHC-I / chaperones / adaptive immune system / antigen processing and presentation
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / Neutrophil degranulation / beta-2-microglobulin binding ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / Neutrophil degranulation / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / early endosome membrane / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-30W / Major histocompatibility complex class I-related protein 1 / Beta-2-microglobulin / Tapasin-related protein / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodSOLUTION NMR / molecular dynamics
AuthorsMcShan, A.C. / Sgourakis, N.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM125034 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R35GM125034-05S United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules.
Authors: McShan, A.C. / Devlin, C.A. / Papadaki, G.F. / Sun, Y. / Green, A.I. / Morozov, G.I. / Burslem, G.M. / Procko, E. / Sgourakis, N.G.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: TAP binding protein-like variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3504
Polymers86,1173
Non-polymers2331
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6870 Å2
ΔGint-20 kcal/mol
Surface area35690 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31724.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Bos taurus (domestic cattle)
Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460, UniProt: C1ITJ8
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11784.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01888
#3: Protein TAP binding protein-like variant


Mass: 42608.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q53GH5
#4: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N5O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-13C HMQC
121anisotropic12D 1H-13C HMQC
131anisotropic23D NOESY HMQC

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Sample preparation

DetailsType: solution
Contents: 100 uM hpMR1 (human platform MR1), 100 uM [U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2] bovine beta 2 microglobulin, 300 uM TAPBPR, 90% H2O/10% D2O
Details: 100 uM AILV bB2m with natural abundance hpMR1, TAPBPR and Ac-6-FP
Label: ILVproS_sample2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMhpMR1 (human platform MR1)natural abundance1
100 uMbovine beta 2 microglobulin[U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2]1
300 uMTAPBPRnatural abundance1
Sample conditionsDetails: buffer: 50 mM NaCl, 20 mM sodium phosphate pH 7.2, 10% D2O
Ionic strength: 50 mM / Label: sampleconditions / pH: 7.2 / Pressure: 1.01325 bar / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
GROMACSv2020.4Department of Biophysical Chemistry, University of Groningen, Netherlandsrefinement
HADDOCKBonvinstructure calculation
NMRFAM-SPARKYWoonghee Lee, Marco Tonelli, and John L. Markleychemical shift assignment
NMRFAM-SPARKYWoonghee Lee, Marco Tonelli, and John L. Markleypeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: HADDOCK in combination with NMR derived chemical shift perturbations was used to generate the initial model of the complex. The TAP binding protein-like variant starting structure is PDB ID ...Details: HADDOCK in combination with NMR derived chemical shift perturbations was used to generate the initial model of the complex. The TAP binding protein-like variant starting structure is PDB ID 5WER chain C. The major histocompatibility complex class I-related gene protein and beta-2-microglobulin are homology modeled based on PDB ID 4PJ5 chain A and chain B.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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