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- PDB-7q99: MHC Class I A02 Allele presenting NLSALGIFST, in complex with Mel5 TCR -

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Basic information

Entry
Database: PDB / ID: 7q99
TitleMHC Class I A02 Allele presenting NLSALGIFST, in complex with Mel5 TCR
Components
  • (Mel5 Human TCR, ...) x 2
  • ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / IMP2 / Diabetes / Autoimmunity
Function / homology
Function and homology information


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 / 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 / Endosomal/Vacuolar 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 / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Wall, A. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.
Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. ...Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. / Legut, M. / Attaf, M. / Hopkins, J.R. / Behiry, E. / Zabkiewicz, J. / Alvares, C. / Lloyd, A. / Rogers, A. / Henley, P. / Fegan, C. / Ottmann, O. / Man, S. / Crowther, M.D. / Donia, M. / Svane, I.M. / Cole, D.K. / Brown, P.E. / Rizkallah, P. / Sewell, A.K.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
D: Mel5 Human TCR, alpha chain
E: Mel5 Human TCR, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0607
Polymers93,9365
Non-polymers1242
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.280, 121.280, 81.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

#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 / 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR


Mass: 1022.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Mel5 Human TCR, ... , 2 types, 2 molecules DE

#4: Protein Mel5 Human TCR, alpha chain


Mass: 21818.934 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 Mel5 Human TCR, beta chain


Mass: 27264.367 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)

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Non-polymers , 2 types, 39 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 25% PEG 4000, 15% Glycerol, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.55→60.65 Å / Num. obs: 70731 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 53.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.075 / Rrim(I) all: 0.211 / Net I/σ(I): 7.2
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 7.4 % / Rmerge(I) obs: 3.86 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1909 / CC1/2: 0.221 / Rpim(I) all: 1.52 / Rrim(I) all: 4.15 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.63 Å60.64 Å
Translation6.63 Å60.64 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HG1
Resolution: 2.55→60.64 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 43.218 / SU ML: 0.375 / SU R Cruickshank DPI: 0.4706 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1905 5 %RANDOM
Rwork0.2183 ---
obs0.2209 36363 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.32 Å2 / Biso mean: 72.408 Å2 / Biso min: 46.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.07 Å20 Å2
3---2.13 Å2
Refinement stepCycle: final / Resolution: 2.55→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6619 0 8 37 6664
Biso mean--83.76 64.7 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156087
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6489252
X-RAY DIFFRACTIONr_angle_other_deg1.1681.58114039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2415823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17722.308390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.616151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9521546
X-RAY DIFFRACTIONr_chiral_restr0.0570.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027828
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021664
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 141 -
Rwork0.442 2313 -
all-2454 -
obs--86.84 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.93170.1255-0.83872.4061-1.09843.05060.05520.0728-0.0760.10660.005-0.2018-0.01220.1744-0.06020.6976-0.0064-0.05320.51250.01940.035368.74616.03515.8547
21.5627-3.08280.93217.7621-1.78332.6950.12590.1644-0.3409-0.2494-0.2054-0.38010.56450.19720.07950.78530.01890.05810.92920.08180.816195.1314-18.417720.4067
36.87380.771.82161.7970.30431.8368-0.0816-0.3120.02930.2009-0.0542-0.5463-0.10020.45240.13580.72620.0156-0.02530.68110.0480.291284.2592-4.570435.7635
41.6459-1.97771.29364.6499-2.11582.87290.12090.1370.2539-0.2998-0.11190.03120.19530.1021-0.0090.6198-0.04120.07550.550.00790.110157.387126.141-6.0354
56.1969-0.15250.21136.20781.58444.24540.11370.21190.5638-0.4836-0.05550.0315-0.5031-0.0997-0.05830.98110.0409-0.050.83020.02590.555841.095853.9103-15.933
60.8315-0.9802-0.32925.3547-0.25850.6886-0.091-0.14390.05090.17140.21680.01840.0086-0.0274-0.12580.55570.0270.00960.6050.01270.416754.9832.705117.0186
73.4051.11842.21784.30441.62055.32310.05840.214-0.1704-0.3842-0.02720.071-0.0096-0.2041-0.03120.53130.10270.04910.6341-0.08020.319236.851.5702-0.0472
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 DIFFRACTION3B1 - 99
5X-RAY DIFFRACTION4D3 - 115
6X-RAY DIFFRACTION5D116 - 200
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 244

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