[English] 日本語
Yorodumi
- PDB-2vlk: The Structural Dynamics and Energetics of an Immunodominant T-cel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vlk
TitleThe Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain
Components
  • BETA-2-MICROGLOBULIN
  • FLU MATRIX PEPTIDE
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • JM22 TCR ALPHA CHAIN
  • JM22 TCR BETA CHAIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / IMMUNE SYSTEM-RECEPTOR-COMPLEX / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / IMMUNE RESPONSE / IMMUNODOMINANCE / DISEASE MUTATION / MEMBRANE / SECRETED / RECEPTOR / GLYCATION / TCR / FLU / MHC / MHC I / T-CELL / COMPLEX
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / RNA binding
Similarity search - Function
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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
UNIDENTIFIED INFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIshizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y.
CitationJournal: Immunity / Year: 2008
Title: The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain
Authors: Ishizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y.
History
DepositionJan 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: FLU MATRIX PEPTIDE
D: JM22 TCR ALPHA CHAIN
E: JM22 TCR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)94,6075
Polymers94,6075
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-74.2 kcal/mol
Surface area47000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)210.800, 47.892, 112.819
Angle α, β, γ (deg.)90.00, 112.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2001-

HOH

-
Components

-
Protein , 4 types, 4 molecules ABDE

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN / MHC CLASS I ANTIGEN A*2


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: HLA-A2, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769
#4: Protein JM22 TCR ALPHA CHAIN


Mass: 22040.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#5: Protein JM22 TCR BETA CHAIN


Mass: 27769.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)

-
Protein/peptide / Non-polymers , 2 types, 216 molecules C

#3: Protein/peptide FLU MATRIX PEPTIDE


Mass: 966.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) UNIDENTIFIED INFLUENZA VIRUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 54.97 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 40395 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 11.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→104.26 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 18.254 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1827 5 %RANDOM
Rwork0.218 ---
obs0.221 34753 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-1.85 Å2
2--0.1 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→104.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 0 215 6833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9329226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4925819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99423.948347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.271151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7061546
X-RAY DIFFRACTIONr_chiral_restr0.1120.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025302
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.22648
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24531
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6520.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.54201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44426623
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17932998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4624.52603
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 149
Rwork0.31 2507
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13470.5074-0.44980.751-0.10923.2919-0.0074-0.03810.023-0.01160.02310.05980.0639-0.1085-0.0157-0.0357-0.0161-0.0284-0.022-0.0012-0.0083141.268540.4386-10.1976
23.2427-1.938-1.60767.88012.9225.8060.0544-0.30740.72140.26490.4154-0.0553-0.4811-0.0629-0.4698-0.05630.09750.1429-0.0171-0.0550.1714130.01854.235120.2651
31.90680.3822-1.34242.2072-0.98335.50630.0041-0.22990.00250.17750.05390.11890.00490.3487-0.058-0.05620.02220.01770.0374-0.0212-0.0214145.759338.512716.3241
48.23353.52021.67972.143-0.87534.3225-0.3126-0.57620.6069-0.1309-0.11690.3753-0.10140.05360.42950.0642-0.0328-0.06020.0604-0.00850.0197143.649639.2781-18.2323
50.558-0.50440.77581.2681-0.35843.6003-0.04560.0608-0.0142-0.06910.00680.0551-0.0987-0.02130.0389-0.0141-0.0375-0.03820.0310.0176-0.001136.006641.3129-45.622
65.324-2.58890.79874.61371.02254.79810.17920.3045-0.4944-0.2356-0.20940.20490.0387-0.3990.0302-0.08330.03440.04950.0414-0.0388-0.0622141.288823.8165-74.1773
71.2505-0.527-0.63863.81452.3024.3292-0.14960.0149-0.04170.18040.14150.00380.36120.14830.00810.00360.0019-0.0429-0.030.029-0.0111150.335125.2797-34.8585
80.3016-0.223-0.27233.3985-2.79056.93360.070.1333-0.031-0.09620.0999-0.18840.1027-0.1719-0.1698-0.10070.0160.0712-0.02080.01370.0686156.01520.9609-65.5354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2A182 - 275
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4C1 - 9
5X-RAY DIFFRACTION5D3 - 115
6X-RAY DIFFRACTION6D116 - 201
7X-RAY DIFFRACTION7E5 - 115
8X-RAY DIFFRACTION8E116 - 244

+
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