[English] 日本語
Yorodumi
- PDB-4jfe: Preservation of peptide specificity during TCR-MHC contact domina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jfe
TitlePreservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR
Components
  • (High Affinity TCR ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma peptide L7A
KeywordsIMMUNE SYSTEM / HLA / TCR / Melanoma / High Affinity
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / 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 / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / complement activation, classical pathway / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / blood microparticle / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation
Similarity search - Function
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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / T cell receptor beta constant 1 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Madura, F. / Sewell, A.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: T-cell receptor specificity maintained by altered thermodynamics.
Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / ...Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / Jakobsen, B.K. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification

-
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: Melanoma peptide L7A
D: High Affinity TCR Alpha Chain
E: High Affinity TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75211
Polymers94,1845
Non-polymers5686
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-117 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.610, 121.610, 82.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 2 types, 2 molecules AB

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Melanoma peptide L7A


Mass: 943.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Heteroclitic L7A variant of Melanoma epitope

-
High Affinity TCR ... , 2 types, 2 molecules DE

#4: Protein High Affinity TCR Alpha Chain


Mass: 21887.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01848*PLUS
#5: Protein High Affinity TCR Beta Chain


Mass: 27522.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01850*PLUS

-
Non-polymers , 3 types, 72 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M BIS TRIS Propane, 20% PEG 4000, 0.2M Ammonium sulphate, 17.4% glycerol, pH 7.0, vapor diffusion, sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorDetector: CCD / Date: Oct 8, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.63→68.13 Å / Num. all: 35640 / Num. obs: 35640 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rsym value: 0.103 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.63-2.78.40.8810.82213626460.881100
2.7-2.788.40.72612125725440.726100
2.78-2.868.40.5791.22071224670.579100
2.86-2.948.30.4561.52028324310.456100
2.94-3.048.30.3372.11954523440.337100
3.04-3.158.30.2552.71869622520.255100
3.15-3.278.30.193.71811921960.19100
3.27-3.48.10.1415.11723421170.141100
3.4-3.558.10.1235.81628920090.123100
3.55-3.7280.0977.21547919360.097100
3.72-3.928.10.0818.31493318550.081100
3.92-4.168.10.0759.21411317420.075100
4.16-4.4580.065101309316290.065100
4.45-4.8180.0678.91228515330.067100
4.81-5.277.90.06110.51120114110.061100
5.27-5.897.90.062101015412830.062100
5.89-6.88.10.06210.3921611380.062100
6.8-8.337.70.04613.874299600.046100
8.33-11.776.80.04115.750797420.04198.8
11.77-54.3455.70.0421523254050.04294.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å68.13 Å
Translation2.7 Å68.13 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→68.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8484 / SU B: 22.405 / SU ML: 0.222 / SU R Cruickshank DPI: 0.7005 / SU Rfree: 0.3191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.7 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1674 5.1 %RANDOM
Rwork0.202 ---
obs0.2044 32992 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 283.61 Å2 / Biso mean: 62.9147 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→68.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 32 66 6734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216885
X-RAY DIFFRACTIONr_bond_other_d0.0010.024664
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9349361
X-RAY DIFFRACTIONr_angle_other_deg0.679311280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4115829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.81123.846351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.748151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2281548
X-RAY DIFFRACTIONr_chiral_restr0.0950.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217750
X-RAY DIFFRACTIONr_gen_planes_other00.021470
X-RAY DIFFRACTIONr_mcbond_it1.10924145
X-RAY DIFFRACTIONr_mcbond_other0.20621668
X-RAY DIFFRACTIONr_mcangle_it2.1536687
X-RAY DIFFRACTIONr_scbond_it3.14742740
X-RAY DIFFRACTIONr_scangle_it5.03662674
LS refinement shellResolution: 2.7→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 123 -
Rwork0.333 2291 -
all-2414 -
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)
13.13860.4218-1.40754.2076-0.68173.4427-0.11710.033-0.27720.04320.0971-0.20260.23410.380.020.02820.03780.03050.1627-0.01760.137754.9756-7.717226.2967
214.5601-4.93552.18146.90110.94556.1383-0.39880.4602-0.1106-0.2621-0.2534-2.09071.33282.14210.65210.87630.49490.35030.96260.46261.687578.5505-34.670720.6952
34.3240.1242-1.68129.28040.15076.9036-0.450.5544-1.092-0.9946-0.16920.1351.46640.00370.61920.43950.06820.14470.365-0.13220.40964.3701-23.67386.4159
44.0377-1.6939-1.8741.01250.91744.7387-0.0582-0.46860.11130.20730.0981-0.0886-0.01040.1626-0.040.115-0.0493-0.02170.12280.02170.10334.81482.786648.0418
516.6357-2.61773.26348.4908-0.479811.7023-0.1981-1.0814-0.14280.60240.10870.3684-0.0219-1.16070.08940.55660.08820.04510.5978-0.03590.20776.881618.888358.2218
610.9863-1.7424-0.42770.8508-0.2942.40970.27770.4908-0.0082-0.3135-0.13850.0797-0.24150.0167-0.13920.20840.0446-0.01520.05260.01390.042229.18256.018825.3662
73.84090.21591.91673.5992.98048.9958-0.181-0.53120.19070.34070.1454-0.1295-0.31870.06090.03550.19270.0647-0.05550.18150.02770.15919.362323.562942.5514
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 - 197
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 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://pdbjlvh1.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