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- PDB-7ow5: Crystal structure of a TCR in complex with HLA-A*11:01 bound to K... -

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Basic information

Entry
Database: PDB / ID: 7ow5
TitleCrystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVVGAGGVGK)
Components
  • Beta-2-microglobulin
  • KRAS peptide (VVVGAGGVGK)
  • MHC class I antigen
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / HLA / KRAS / TCR
Function / homology
Function and homology information


myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / tertiary granule membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling ...myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / tertiary granule membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / VEGFR2 mediated cell proliferation / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to iron(III) ion / Signaling by high-kinase activity BRAF mutants / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Constitutive Signaling by EGFRvIII / negative regulation of forebrain neuron differentiation / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / Signaling by ERBB2 KD Mutants / MHC class I peptide loading complex / Signaling by SCF-KIT / 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 / Regulation of RAS by GAPs / positive regulation of T cell mediated cytotoxicity / specific granule lumen / RAS processing / recycling endosome membrane / Negative regulation of MAPK pathway
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / : / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains / Small GTPase / Ras family ...Small GTPase, Ras-type / small GTPase Ras family profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / : / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / MHC class I alpha chain, alpha1 alpha2 domains / Small GTPase / Ras family / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rab subfamily of small GTPases / 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 / : / Small GTP-binding protein 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / GTPase NRas / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsKaruppiah, V. / Robinson, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen
Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / ...Authors: Poole, A. / Karuppiah, V. / Hartt, A. / Haidar, J.N. / Moureau, S. / Dobrzycki, T. / Hayes, C. / Rowley, C. / Dias, J. / Harper, S. / Barnbrook, K. / Hock, M. / Coles, C. / Yang, W. / Aleksic, M. / Lin, A.B. / Robinson, R. / Dukes, J.D. / Liddy, N. / Van der Kamp, M. / Plowman, G.D. / Vuidepot, A. / Cole, D.K. / Whale, A.D. / Chillakuri, C.
History
DepositionJun 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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: KRAS peptide (VVVGAGGVGK)
D: TCR alpha
E: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4578
Polymers95,1695
Non-polymers2883
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.552, 145.552, 120.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen


Mass: 31952.164 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: A0A583ZB34
#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 TCR alpha


Mass: 22891.230 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 TCR beta


Mass: 27602.912 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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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide KRAS peptide (VVVGAGGVGK) / Transforming protein N-Ras / GTPase NRas


Mass: 843.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01111, small monomeric GTPase

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Non-polymers , 2 types, 20 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→65.09 Å / Num. obs: 41420 / % possible obs: 100 % / Redundancy: 26.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.03 / Rrim(I) all: 0.153 / Net I/σ(I): 14.7
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 27.6 % / Rmerge(I) obs: 5.709 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2057 / CC1/2: 0.343 / Rpim(I) all: 1.102 / Rrim(I) all: 5.816 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HN7, 6BJ2, 2F53

2hn7

6bj2

2f53


Resolution: 2.58→65.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 40.008 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27356 2127 5.1 %RANDOM
Rwork0.20595 ---
obs0.2094 39259 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.58→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 15 17 6624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156088
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6519230
X-RAY DIFFRACTIONr_angle_other_deg1.2271.58414030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7465816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80722.267397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.306151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8431548
X-RAY DIFFRACTIONr_chiral_restr0.0690.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021669
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_it2.7755.3243279
X-RAY DIFFRACTIONr_mcbond_other2.7735.3243278
X-RAY DIFFRACTIONr_mcangle_it4.3827.9824087
X-RAY DIFFRACTIONr_mcangle_other4.3817.9834088
X-RAY DIFFRACTIONr_scbond_it35.5673514
X-RAY DIFFRACTIONr_scbond_other2.7835.5373500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4848.1975124
X-RAY DIFFRACTIONr_long_range_B_refined6.44557.9467017
X-RAY DIFFRACTIONr_long_range_B_other6.44557.9567018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.646 Å
RfactorNum. reflection% reflection
Rfree0.488 163 -
Rwork0.498 2869 -
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)
11.22411.54370.06662.9537-0.15830.9412-0.05240.171-0.1183-0.21980.1338-0.03330.05670.0349-0.08150.43020.15470.02210.46-0.1050.0531-50.31661.3563-2.1114
21.14940.59890.32255.93751.95452.0705-0.18430.2092-0.3691-0.20670.1653-0.56490.28310.43060.01910.49550.12890.07820.4996-0.15160.4348-38.0676-13.1308-6.3009
33.40951.5128-0.61325.88276.05727.95190.1871-0.0326-0.2497-0.42260.0369-0.3537-0.5077-0.1419-0.2240.42610.06490.14140.48740.09010.085-43.683619.48480.4651
40.51481.46920.33366.30480.59580.6431-0.1330.11940.4541-0.13230.00110.94-0.35370.02910.13190.37060.01770.03170.59350.05490.6675-40.964456.355-1.2109
50.97061.82530.74184.43510.67121.3695-0.060.22110.0941-0.0486-0.10160.1163-0.02890.43920.16170.15170.01920.01920.57440.07420.0265-21.425755.89020.586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 276
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D1 - 195
5X-RAY DIFFRACTION5E0 - 245

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