[English] 日本語
Yorodumi
- PDB-6tmo: Structure determination of an enhanced affinity TCR, a24b17, in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tmo
TitleStructure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01 presenting a MART-1 peptide, EAAGIGILTV
Components
  • Alpha chain of engineered high affinity T-cell receptor
  • Beta chain of high affinity engineered T-cell receptor
  • Beta-2-microglobulin
  • EAAGIGILTV
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / High affinity / T-cell receptor
Function / homology
Function and homology information


melanosome membrane / Regulation of MITF-M-dependent genes involved in pigmentation / : / : / 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 ...melanosome membrane / Regulation of MITF-M-dependent genes involved in pigmentation / : / : / 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 / 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 / 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 T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / 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 / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / melanosome / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Protein melan-A / Protein melan-A / 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 / : ...Protein melan-A / Protein melan-A / 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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Mol Ther Oncolytics / Year: 2020
Title: Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy.
Authors: Crean, R.M. / MacLachlan, B.J. / Madura, F. / Whalley, T. / Rizkallah, P.J. / Holland, C.J. / McMurran, C. / Harper, S. / Godkin, A. / Sewell, A.K. / Pudney, C.R. / van der Kamp, M.W. / Cole, D.K.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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 1.3Nov 13, 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: MHC class I antigen
B: Beta-2-microglobulin
C: EAAGIGILTV
D: Alpha chain of engineered high affinity T-cell receptor
E: Beta chain of high affinity engineered T-cell receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,91725
Polymers94,0525
Non-polymers1,86520
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-81 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.490, 121.490, 82.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#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 (E. coli) / References: UniProt: P61769
#4: Protein Alpha chain of engineered high affinity T-cell receptor


Mass: 21887.055 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 Beta chain of high affinity engineered T-cell receptor


Mass: 27391.492 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 , 1 types, 1 molecules C

#3: Protein/peptide EAAGIGILTV


Mass: 943.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655*PLUS

-
Non-polymers , 5 types, 408 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 0.2 M Ammonium Sulphate 15 % PEG 4000 8.7% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→54.332 Å / Num. obs: 69920 / % possible obs: 99.4 % / Redundancy: 8.3 % / Biso Wilson estimate: 33.3 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.096 / Rsym value: 0.084 / Net I/av σ(I): 7.8 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.158.40.71314282951100.2770.8070.7133.699
2.15-2.218.40.5941.24202350000.2290.670.5944.399.1
2.21-2.288.40.5071.44052448400.1970.5740.507599.2
2.28-2.358.40.4171.83995047470.1620.4730.4175.999.1
2.35-2.428.40.36623885146110.1420.4150.3666.699.1
2.42-2.518.40.2912.53728944290.1130.330.291899.2
2.51-2.68.40.2333.23607542920.0910.2640.2339.699.6
2.6-2.718.30.1953.83444141300.0760.2210.19511.299.6
2.71-2.838.40.1554.83333139820.060.1760.15513.299.6
2.83-2.978.40.1236.13210538190.0480.1390.1231699.4
2.97-3.138.40.09383027836220.0360.1050.09319.399.7
3.13-3.328.30.0759.82834734170.0290.0850.07522.999.7
3.32-3.558.20.06211.72646432220.0240.070.0622799.8
3.55-3.838.20.05313.22468130180.0210.060.0533199.8
3.83-4.28.20.04714.12270527800.0180.0520.04734.299.8
4.2-4.780.0415.72015225080.0160.0440.0437.299.9
4.7-5.428.20.03717.31829622400.0140.0410.03737.8100
5.42-6.648.30.03917.21560718860.0150.0440.03937.1100
6.64-9.3980.03319.91175814670.0130.0370.03338.399.5
9.39-54.3327.40.02922.759118000.0120.0330.02939.395.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å54.33 Å
Translation2.5 Å54.33 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGI

3hgi


Resolution: 2.1→54.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.782 / SU ML: 0.093 / SU R Cruickshank DPI: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 3532 5.1 %RANDOM
Rwork0.1725 ---
obs0.1744 66386 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 180.17 Å2 / Biso mean: 40.285 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.1→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 116 388 7132
Biso mean--55.61 43.39 -
Num. residues----827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216952
X-RAY DIFFRACTIONr_bond_other_d0.0010.024754
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9419431
X-RAY DIFFRACTIONr_angle_other_deg0.746311484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6465828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00723.846351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.974151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7381548
X-RAY DIFFRACTIONr_chiral_restr0.1290.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217748
X-RAY DIFFRACTIONr_gen_planes_other00.021471
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 254 -
Rwork0.216 4845 -
all-5099 -
obs--100 %
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)
12.7702-0.00450.24112.03990.84922.09550.01570.03880.09010.0114-0.01260.106-0.1589-0.1223-0.0030.11070.00780.02370.0167-0.01440.0574-7.787154.816156.9185
24.8688-2.4819-0.14838.0270.98586.2015-0.1706-0.11171.5814-0.5214-0.36940.3454-1.6062-0.81530.540.53130.2342-0.28370.4735-0.27330.98-34.273478.733562.063
35.54520.94290.52392.98581.70175.1228-0.0396-0.71010.05580.2564-0.39220.63030.1557-1.21690.43180.15-0.00280.04470.368-0.11720.2409-23.63164.229576.8703
41.4269-0.9798-0.52593.35020.7533.27340.05160.2050.0637-0.3487-0.059-0.0888-0.108-0.02630.00740.0727-0.0114-0.01840.0360.00770.06372.910634.808835.2926
57.13250.4573-1.098210.8827-4.75588.36430.22540.1687-0.4183-0.9564-0.4063-0.14671.06470.09060.18090.72130.15080.05590.3908-0.0030.265419.45886.874125.3428
61.0216-1.84420.29336.25930.54331.6309-0.1452-0.2058-0.04420.50520.1734-0.02090.05340.0982-0.02820.09360.0193-0.02350.1099-0.0030.06336.18929.167157.8064
73.1598-0.2581-1.48554.4412-2.23676.88470.28490.44220.1123-0.7961-0.3587-0.28650.01920.26580.07380.23020.12020.01950.15550.06220.186623.93719.49841.0971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 200
7X-RAY DIFFRACTION6E1 - 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