[English] 日本語
Yorodumi
- PDB-5brz: MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5brz
TitleMAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR
  • HLA class I histocompatibility antigen, A-1 alpha chain
  • Protein TRAV21,T-cell receptor alpha chain C region
  • Protein TRBV5-1,Human nkt tcr beta chain
KeywordsIMMUNE SYSTEM / Immuno pMHC TCR MAGE
Function / homology
Function and homology information


caspase binding / alpha-beta T cell receptor complex / negative regulation of protein processing / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation ...caspase binding / alpha-beta T cell receptor complex / negative regulation of protein processing / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / negative regulation of autophagy / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / histone deacetylase binding / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21 / T cell receptor beta variable 5-1 / Human nkt tcr beta chain / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Melanoma-associated antigen 3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsRaman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / LeProvost, G. / Mahon, T. / Hickman, E. / LomaX, M. ...Raman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / LeProvost, G. / Mahon, T. / Hickman, E. / LomaX, M. / Oates, J. / Hassan, N. / Vuidepot, A. / Sami, M. / Cole, D.K. / Jakobsen, B.K.
CitationJournal: Sci Rep / Year: 2016
Title: Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy.
Authors: Raman, M.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / Le Provost, G.S. / Todorov, P. / Baston, E. / Hickman, E. / Mahon, T. / Hassan, N. / Vuidepot, A. / ...Authors: Raman, M.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / Le Provost, G.S. / Todorov, P. / Baston, E. / Hickman, E. / Mahon, T. / Hassan, N. / Vuidepot, A. / Sami, M. / Cole, D.K. / Jakobsen, B.K.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
C: GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR
D: Protein TRAV21,T-cell receptor alpha chain C region
E: Protein TRBV5-1,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,91312
Polymers93,2415
Non-polymers6727
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-154 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.590, 47.500, 119.250
Angle α, β, γ (deg.)90.000, 109.120, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A-1 alpha chain / MHC class I antigen A*1


Mass: 31734.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / 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 (E. coli) / References: UniProt: P61769
#4: Protein Protein TRAV21,T-cell receptor alpha chain C region


Mass: 21451.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV21, TRAC, TCRA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279, UniProt: P01848
#5: Protein Protein TRBV5-1,Human nkt tcr beta chain / V_segment translation product


Mass: 27132.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV5S1A1T, TRBV5-1, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A578, UniProt: K7N5M4

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR


Mass: 1043.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43357*PLUS

-
Non-polymers , 2 types, 24 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M HEPES pH7, 15% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.62→82.01 Å / Num. obs: 27833 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.064 / Net I/σ(I): 12.4 / Num. measured all: 99682
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.62-2.693.70.9151.9744720050.450.58899.7
11.72-82.013.30.0239.711133370.9990.01393

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.62 Å82.01 Å
Translation2.62 Å82.01 Å

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W72 and 3O4L

1w72

3o4l


Resolution: 2.62→82.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2497 / WRfactor Rwork: 0.1761 / FOM work R set: 0.7991 / SU B: 30.693 / SU ML: 0.29 / SU R Cruickshank DPI: 0.3013 / SU Rfree: 0.3592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1399 5 %RANDOM
Rwork0.1934 ---
obs0.1971 26433 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.93 Å2 / Biso mean: 62.589 Å2 / Biso min: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-2.06 Å2
2--2.19 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.62→82.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 35 17 6618
Biso mean--91.59 41.99 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196771
X-RAY DIFFRACTIONr_bond_other_d0.0010.026099
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9399198
X-RAY DIFFRACTIONr_angle_other_deg0.841314040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9245817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0623.757346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.193151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911553
X-RAY DIFFRACTIONr_chiral_restr0.0930.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021658
X-RAY DIFFRACTIONr_mcbond_it1.4032.7883283
X-RAY DIFFRACTIONr_mcbond_other1.4032.7873282
X-RAY DIFFRACTIONr_mcangle_it2.3364.1764095
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 88 -
Rwork0.315 1915 -
all-2003 -
obs--99.7 %
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)
14.06020.44760.17521.7629-0.32874.0922-0.0287-0.2311-0.130.0294-0.0214-0.01170.0907-0.1950.05010.0428-0.02280.07580.0941-0.02270.1427139.575235.6415165.2618
22.35390.40831.84616.38342.89075.3505-0.3315-0.36240.77840.4505-0.150.3405-0.898-0.52860.48150.40010.12010.07820.444-0.10140.4687138.564750.1081198.4523
32.70.0125-0.28863.5744-1.81398.0576-0.0065-0.3052-0.20890.5020.027-0.32860.16880.3443-0.02040.12720.00440.01730.1729-0.04920.2335153.665435.4344189.0251
43.76410.62733.74893.26342.43927.40660.1024-0.12960.0684-0.2642-0.16810.56680.0687-0.69760.06580.1048-0.00570.06160.27640.0190.362116.813131.2537142.131
55.2202-3.2382-0.31587.87640.24964.128-0.1507-0.0756-0.28630.20910.06870.58860.1345-0.47330.0820.5412-0.0364-0.20530.7322-0.00310.5837106.184714.6519113.1312
62.05590.93751.01476.10571.70253.99770.05280.056-0.1137-0.00920.1189-0.04060.4981-0.0266-0.17170.1570.01810.08040.15310.00340.1382134.075415.9466141.7681
75.2164-2.50463.41484.3005-4.31166.42960.24810.54840.0431-0.4169-0.13660.31580.38980.1596-0.11160.47440.00860.00970.3278-0.08330.2611122.691812.0844113.4509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 210
7X-RAY DIFFRACTION6E0 - 115
8X-RAY DIFFRACTION7E116 - 246

+
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