[English] 日本語
Yorodumi
- PDB-7n4k: 6218 TCR in complex with H2-Db PA 224 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n4k
Title6218 TCR in complex with H2-Db PA 224
Components
  • (Fusion protein of T cell receptor ...) x 2
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Peptide from Polymerase acidic protein
KeywordsIMMUNE SYSTEM / Major Histocompatibility complex / MHC / mouse / Influenza A / polymerase acidic protein / H2Db / T cell receptor / PA224-233
Function / homology
Function and homology information


cap snatching / immune system process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding ...cap snatching / immune system process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / Hydrolases; Acting on ester bonds / host cell cytoplasm / learning or memory / Amyloid fiber formation / viral translational frameshifting / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / viral RNA genome replication / focal adhesion / symbiont-mediated suppression of host gene expression / DNA-templated transcription / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
T cell receptor alpha variable 21-DV12 / T cell receptor beta, variable 29 / Human nkt tcr beta chain / T-cell receptor, sp3.4 alpha chain / Polymerase acidic protein / H-2 class I histocompatibility antigen, D-B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSzeto, C. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Nat Commun / Year: 2022
Title: Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.
Authors: Szeto, C. / Zareie, P. / Wirasinha, R.C. / Zhang, J.B. / Nguyen, A.T. / Riboldi-Tunnicliffe, A. / La Gruta, N.L. / Gras, S. / Daley, S.R.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Peptide from Polymerase acidic protein
D: Fusion protein of T cell receptor alpha variable 21-DV12 and T-cell receptor, sp3.4 alpha chain
E: Fusion protein of T cell receptor beta, variable 29 and Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9249
Polymers94,8325
Non-polymers924
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.140, 72.530, 107.720
Angle α, β, γ (deg.)90.000, 101.360, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32184.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Peptide from Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 1186.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: O89752

-
Fusion protein of T cell receptor ... , 2 types, 2 molecules DE

#4: Protein Fusion protein of T cell receptor alpha variable 21-DV12 and T-cell receptor, sp3.4 alpha chain / T-cell receptor / sp3.4 beta chain


Mass: 22005.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav21-dv12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A075B6C4, UniProt: K7N5N2
#5: Protein Fusion protein of T cell receptor beta, variable 29 and Human nkt tcr beta chain


Mass: 27575.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trbv29, B2M, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0G2LB96, UniProt: K7N5M4

-
Non-polymers , 2 types, 402 molecules

#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2 M NaF, 0.05 M NaForm, 1% 1,5-Diaminopentane dihydrochloride

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.85→44.07 Å / Num. obs: 69886 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.056 / Rrim(I) all: 0.107 / Net I/σ(I): 8.7 / Num. measured all: 247148 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.893.60.6691549142840.6670.4130.7881.9100
9.06-44.073.30.03920966270.9590.0260.04724.699.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PQY

3pqy


Resolution: 1.85→44.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3484 4.99 %RANDOM
Rwork0.186 ---
obs0.187 69854 100 %-
Displacement parametersBiso max: 106.69 Å2 / Biso mean: 27.03 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-2.7676 Å20 Å2-0.4722 Å2
2---4.1019 Å20 Å2
3---1.3343 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.85→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 4 398 7050
Biso mean--38.8 29.07 -
Num. residues----822
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2395SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1202HARMONIC5
X-RAY DIFFRACTIONt_it6955HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion869SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8019SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6955HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9465HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion19.04
LS refinement shellResolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2481 57 4.08 %
Rwork0.2207 1341 -
all0.2218 1398 -
obs--99.85 %

+
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