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- PDB-7pb2: Crystal structure of JDI TCR in complex with HLA-A*11:01 bound to... -

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Basic information

Entry
Database: PDB / ID: 7pb2
TitleCrystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)
Components
  • Beta-2-microglobulin
  • KRAS G12D peptide (VVVGADGVGK)
  • MHC class I antigen
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / HLA / T cell receptor / KRAS
Function / homology
Function and homology information


myoblast differentiation / antigen processing and presentation of peptide antigen via MHC class I / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS ...myoblast differentiation / antigen processing and presentation of peptide antigen via MHC class I / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / 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 / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / 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 / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / : / : / positive regulation of receptor binding / early endosome lumen / VEGFR2 mediated cell proliferation / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / small monomeric GTPase / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / RAF activation / 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 / Signaling by ERBB2 TMD/JMD mutants / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / Signaling by high-kinase activity BRAF mutants / MHC class I peptide loading complex / response to molecule of bacterial origin / Signaling by SCF-KIT / HFE-transferrin receptor complex / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / T cell mediated cytotoxicity / Signaling by ERBB2 ECD mutants / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / Signaling by ERBB2 KD Mutants / 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
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Small GTPase, Ras-type / small GTPase Ras family profile. / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Class I Histocompatibility antigen, domains alpha 1 and 2 / Small GTPase / Ras family / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Rab subfamily of small GTPases / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
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: 3.41 Å
AuthorsColes, C.H. / Karuppiah, 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
DepositionJul 30, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 G12D peptide (VVVGADGVGK)
D: TCR alpha
E: TCR beta
F: MHC class I antigen
G: Beta-2-microglobulin
H: KRAS G12D peptide (VVVGADGVGK)
I: TCR alpha
J: TCR beta


Theoretical massNumber of molelcules
Total (without water)189,95010
Polymers189,95010
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: KRAS G12D peptide (VVVGADGVGK)
D: TCR alpha
E: TCR beta


Theoretical massNumber of molelcules
Total (without water)94,9755
Polymers94,9755
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: KRAS G12D peptide (VVVGADGVGK)
I: TCR alpha
J: TCR beta


Theoretical massNumber of molelcules
Total (without water)94,9755
Polymers94,9755
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.366, 208.366, 124.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA2 - 2752 - 275
21SERSERGLUGLUFF2 - 2752 - 275
12GLNGLNARGARGBB2 - 973 - 98
22GLNGLNARGARGGG2 - 973 - 98
13GLNGLNSERSERDD2 - 1832 - 183
23GLNGLNSERSERII2 - 1832 - 183
14ASNASNALAALAEE1 - 2441 - 244
24ASNASNALAALAJJ1 - 2441 - 244

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein MHC class I antigen


Mass: 31952.164 Da / Num. of mol.: 2
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.: 2
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
#3: Protein/peptide KRAS G12D peptide (VVVGADGVGK) / Transforming protein N-Ras / GTPase NRas


Mass: 901.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01111, small monomeric GTPase
#4: Protein TCR alpha


Mass: 22749.033 Da / Num. of mol.: 2
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: 27493.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 3.41→147.77 Å / Num. obs: 38015 / % possible obs: 99.98 % / Redundancy: 28.5 % / CC1/2: 1 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.026 / Rrim(I) all: 0.138 / Net I/σ(I): 18.7
Reflection shellResolution: 3.41→3.47 Å / Redundancy: 17.5 % / Rmerge(I) obs: 2.603 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1869 / CC1/2: 0.618 / Rpim(I) all: 0.622 / Rrim(I) all: 2.68 / % possible all: 99.52

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UQ2, 4JRX, 4X6B

4uq2

4jrx

4x6b


Resolution: 3.41→147.77 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.929 / SU B: 66.141 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1864 4.9 %RANDOM
Rwork0.22783 ---
obs0.22912 36110 99.87 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 3.41→147.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12801 0 0 0 12801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313148
X-RAY DIFFRACTIONr_bond_other_d0.0010.01811769
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.65217866
X-RAY DIFFRACTIONr_angle_other_deg1.041.58327116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99251579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39122.252777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16152104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0791594
X-RAY DIFFRACTIONr_chiral_restr0.0340.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023241
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89110.06
12F89110.06
21B29450.05
22G29450.05
31D47610.08
32I47610.08
41E76710.05
42J76710.05
LS refinement shellResolution: 3.41→3.497 Å
RfactorNum. reflection% reflection
Rfree0.321 165 -
Rwork0.359 2585 -
obs--99.57 %
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)
12.37890.60670.50961.65440.72231.747-0.15960.24950.0691-0.25070.19420.0046-0.28780.3601-0.03460.7577-0.09760.09040.41910.1520.0887142.80263.52-125.671
22.9740.496-0.0541.95760.05661.57290.17870.57930.8867-0.22840.01930.1833-0.6236-0.0234-0.1981.0543-0.20860.03750.45740.2410.5556145.39782.369-129.97
31.72290.8498-3.53270.4507-2.478829.16420.13430.2850.7480.03450.17190.3441.30160.069-0.30620.65240.13820.05520.40370.29620.4893125.03956.418-123.161
48.2122.1645-2.21.21810.38482.066-0.16540.5539-1.2563-0.0469-0.1126-0.30040.1479-0.57670.2780.57580.0532-0.01520.59350.20570.679497.67835.733-125.721
54.67451.7993-2.3771.139-0.54852.01020.03811.07190.0679-0.25280.0427-0.0085-0.3437-0.8362-0.08080.57820.2758-0.03250.72770.17310.221683.11449.633-122.097
62.4534-0.97550.26521.4269-0.50441.33520.0046-0.11380.70870.17650.05650.1695-0.4736-0.4827-0.06110.90670.20340.17160.5268-0.02250.460375.1868.458-90.867
71.5057-0.94150.07430.6304-0.03590.0394-0.2631-0.57411.23630.10360.2257-0.7395-0.2233-0.04080.03741.50940.30330.08660.6615-0.28071.467575.38587.343-85.727
81.5712.12732.18862.982.99893.06370.1968-0.00090.03180.2489-0.1382-0.12650.2895-0.0238-0.05850.72020.12680.11670.3341-0.03280.619291.61358.813-92.815
98.2271-3.6359-1.64511.92210.52561.8165-0.1599-0.0804-1.2370.2218-0.08580.370.27330.27690.24580.6047-0.12480.01880.28880.01580.5118117.34232.884-90.709
103.53-1.8604-1.08031.67050.59171.55090.0196-0.23330.08690.213-0.0289-0.067-0.31090.38730.00930.5364-0.28450.01510.32490.0430.0866131.96645.8-94.136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B2 - 98
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D2 - 184
5X-RAY DIFFRACTION5E1 - 244
6X-RAY DIFFRACTION6F2 - 275
7X-RAY DIFFRACTION7G2 - 98
8X-RAY DIFFRACTION8H1 - 10
9X-RAY DIFFRACTION9I2 - 196
10X-RAY DIFFRACTION10J1 - 244

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