[English] 日本語
Yorodumi
- PDB-7rno: Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated do... -

+
Open data


ID or keywords:

Loading...

-
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-microglobulinBeta-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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / beta-2-microglobulin binding / T cell receptor binding / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / 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 / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
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 / Immunoglobulin subtype ...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 / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Similarity search - Domain/homology
Chem-30W / Major histocompatibility complex class I-related gene protein / Beta-2-microglobulin / TAP binding protein-like variant / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 (cattle)
Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460, UniProt: C1ITJ8
#2: Protein Beta-2-microglobulin / 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 (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

-
Experimental details

-
Experiment

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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more