[English] 日本語
Yorodumi
- PDB-5nqk: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nqk
Titlehuman 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / Melan-A/MART-1 PEPTIDE / DECAPEPTIDE / MHC CLASS I / HLA-A2 / T cell receptor
Function / homology
Function and homology information


melanosome membrane / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / T cell receptor complex ...melanosome membrane / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / T cell receptor complex / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / Regulation of MITF-M-dependent genes involved in pigmentation / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / Co-inhibition by PD-1 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / immune system process / detection of bacterium / T cell receptor binding / endomembrane system / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / 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 / trans-Golgi network / MHC class II protein complex / 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 iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / melanosome / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
Protein melan-A / Protein melan-A / : / : / 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 ...Protein melan-A / Protein melan-A / : / : / 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/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 beta variable 19 / T cell receptor alpha variable 12-2 / T cell receptor alpha joining 45 / TRB protein / : / T cell receptor beta variable 19 / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsExertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D.
CitationJournal: To Be Published
Title: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Authors: Exertier, C. / Reiser, J.-B. / Housset, D.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
P: Melanoma antigen recognized by T-cells 1
A: T-cell receptor alpha variable 12-2,T-cell receptor alpha joining 45,T-cell receptor alpha chain C region
B: T-cell receptor beta variable 19,TRB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2506
Polymers96,2275
Non-polymers231
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-68 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.180, 49.720, 95.720
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 2 molecules HL

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31979.367 Da / Num. of mol.: 1 / Mutation: A245V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Variant (production host): X90F LAQQ1 / 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) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Variant (production host): X90F LAQQ1 / References: UniProt: P61769

-
T-cell receptor ... , 2 types, 2 molecules AB

#4: Protein T-cell receptor alpha variable 12-2,T-cell receptor alpha joining 45,T-cell receptor alpha chain C region / 199.54 TCR ALPHA CHAIN (TRAJ 12-2 / TRAJ 45) / T-CELL RECEPTOR / 199.54 TCR ALPHA CHAIN (TRAJ 12-2 / TRAJ 45)


Mass: 23090.320 Da / Num. of mol.: 1 / Mutation: T158C,T158C,T158C
Source method: isolated from a genetically manipulated source
Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRAV 12-2 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (ENDGGGCK) TO ENHANCE ALPHA-BETA CHAIN PAIRING.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2, TRAJ45, TRAC / Plasmid: pJEXPRESS414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL
References: UniProt: A0A075B6T6, UniProt: A0A075B6X0, UniProt: A0A1B0GUM0, UniProt: P01848*PLUS
#5: Protein T-cell receptor beta variable 19,TRB protein / V_SEGMENT TRANSLATION PRODUCT / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2) / 199.16 ...V_SEGMENT TRANSLATION PRODUCT / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2) / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2)


Mass: 28292.430 Da / Num. of mol.: 1 / Mutation: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C
Source method: isolated from a genetically manipulated source
Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRBV 19 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (DQDRGGGCD) TO ENHANCE ALPHA-BETA CHAIN PAIRING.
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV17S1A1T, TRBV19, TRB / Plasmid: pJEXPRESS414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL
References: UniProt: A0A5B3, UniProt: A0A0C4ZKA8, UniProt: A0A075B6N1*PLUS

-
Protein/peptide / Non-polymers , 2 types, 2 molecules P

#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / ANTIGEN LB39-AA / ANTIGEN SK29-AA / PROTEIN MELAN-A / MELAN-A/MART-1 (26-35) DECAPEPTIDE


Mass: 985.176 Da / Num. of mol.: 1 / Mutation: A27L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655*PLUS
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350 11%, bis-tris propane pH 6.5 0.1M, KNa tartrate 0.1M

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.25→48.53 Å / Num. obs: 16830 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rsym value: 0.173 / Net I/σ(I): 6.28
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 3.43 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1236 / CC1/2: 0.523 / Rsym value: 1.611 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NHT

5nht


Resolution: 3.25→48.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 50.604 / SU ML: 0.742 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31617 722 5 %RANDOM
Rwork0.22357 ---
obs0.22803 13863 85.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 109.51 Å2
Baniso -1Baniso -2Baniso -3
1--8.71 Å20 Å2-5.34 Å2
2--9.62 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 3.25→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 1 0 6604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196782
X-RAY DIFFRACTIONr_bond_other_d0.0020.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9299202
X-RAY DIFFRACTIONr_angle_other_deg0.926313735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35524350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4361546
X-RAY DIFFRACTIONr_chiral_restr0.0770.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.22711.1143292
X-RAY DIFFRACTIONr_mcbond_other5.22711.1163293
X-RAY DIFFRACTIONr_mcangle_it8.8316.6564107
X-RAY DIFFRACTIONr_mcangle_other8.82916.6564107
X-RAY DIFFRACTIONr_scbond_it4.29911.373490
X-RAY DIFFRACTIONr_scbond_other4.29911.3683488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.46516.9415095
X-RAY DIFFRACTIONr_long_range_B_refined12.6517326
X-RAY DIFFRACTIONr_long_range_B_other12.657327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.248→3.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 37 -
Rwork0.483 768 -
obs--64.14 %

+
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