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- PDB-9iky: Crystal structure of 1-2C-T96F TCR in complex with HLA-A*11:01 bo... -

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Basic information

Entry
Database: PDB / ID: 9iky
TitleCrystal structure of 1-2C-T96F TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK)
Components
  • 1-2C-T96F TCR alpha chain
  • 1-2C-T96F TCR beta chain
  • Beta-2-microglobulin
  • MHC class I antigen
  • VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
KeywordsIMMUNE SYSTEM / TCR-pHLA Complex structure / KRAS-G12V9 / T cell immunity / Tumor neoantigen
Function / homology
Function and homology information


: / : / 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 ...: / : / 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 / 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 / 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 / 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
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. ...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)
Mus musculus (house mouse)
Kirsten murine sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsMa, K.K. / Tan, S.G. / Gao, G.F. / Chai, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169208 China
National Natural Science Foundation of China (NSFC)32222031 China
CitationJournal: Adv Sci / Year: 2025
Title: An Engineered Soluble Single-Chain TCR Engager for KRAS-G12V Specific Tumor Immunotherapy.
Authors: Ma, K. / Wang, J. / Jiang, M. / He, J. / Li, F. / Lu, D. / Su, C. / Chai, Y. / Jin, W. / Chen, Y. / Zhang, C.W.H. / Ma, X. / Tan, H. / Gao, G.F. / Tan, S.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
o: MHC class I antigen
p: Beta-2-microglobulin
q: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
r: 1-2C-T96F TCR alpha chain
s: 1-2C-T96F TCR beta chain
A: MHC class I antigen
B: Beta-2-microglobulin
C: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
D: 1-2C-T96F TCR alpha chain
E: 1-2C-T96F TCR beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
I: 1-2C-T96F TCR alpha chain
J: 1-2C-T96F TCR beta chain
K: MHC class I antigen
L: Beta-2-microglobulin
M: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
N: 1-2C-T96F TCR alpha chain
O: 1-2C-T96F TCR beta chain
P: MHC class I antigen
Q: Beta-2-microglobulin
R: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
S: 1-2C-T96F TCR alpha chain
T: 1-2C-T96F TCR beta chain
U: MHC class I antigen
V: Beta-2-microglobulin
W: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
X: 1-2C-T96F TCR alpha chain
Y: 1-2C-T96F TCR beta chain
Z: MHC class I antigen
a: Beta-2-microglobulin
b: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
c: 1-2C-T96F TCR alpha chain
d: 1-2C-T96F TCR beta chain
e: MHC class I antigen
f: Beta-2-microglobulin
g: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
h: 1-2C-T96F TCR alpha chain
i: 1-2C-T96F TCR beta chain
j: MHC class I antigen
k: Beta-2-microglobulin
l: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
m: 1-2C-T96F TCR alpha chain
n: 1-2C-T96F TCR beta chain
t: MHC class I antigen
u: Beta-2-microglobulin
v: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
w: 1-2C-T96F TCR alpha chain
x: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)944,94650
Polymers944,94650
Non-polymers00
Water00
1
o: MHC class I antigen
p: Beta-2-microglobulin
q: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
r: 1-2C-T96F TCR alpha chain
s: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MHC class I antigen
B: Beta-2-microglobulin
C: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
D: 1-2C-T96F TCR alpha chain
E: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: MHC class I antigen
G: Beta-2-microglobulin
H: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
I: 1-2C-T96F TCR alpha chain
J: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: MHC class I antigen
L: Beta-2-microglobulin
M: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
N: 1-2C-T96F TCR alpha chain
O: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
P: MHC class I antigen
Q: Beta-2-microglobulin
R: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
S: 1-2C-T96F TCR alpha chain
T: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
U: MHC class I antigen
V: Beta-2-microglobulin
W: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
X: 1-2C-T96F TCR alpha chain
Y: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Z: MHC class I antigen
a: Beta-2-microglobulin
b: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
c: 1-2C-T96F TCR alpha chain
d: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
e: MHC class I antigen
f: Beta-2-microglobulin
g: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
h: 1-2C-T96F TCR alpha chain
i: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
e: MHC class I antigen
f: Beta-2-microglobulin
g: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
h: 1-2C-T96F TCR alpha chain
i: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
j: MHC class I antigen
k: Beta-2-microglobulin
l: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
m: 1-2C-T96F TCR alpha chain
n: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
t: MHC class I antigen
u: Beta-2-microglobulin
v: VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS
w: 1-2C-T96F TCR alpha chain
x: 1-2C-T96F TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4955
Polymers94,4955
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.775, 157.773, 193.023
Angle α, β, γ (deg.)103.030, 101.920, 82.170
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
MHC class I antigen


Mass: 31855.051 Da / Num. of mol.: 10
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: A0A6M6CC39
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 10
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
VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS


Mass: 785.951 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) Kirsten murine sarcoma virus
#4: Protein
1-2C-T96F TCR alpha chain


Mass: 22900.363 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#5: Protein
1-2C-T96F TCR beta chain


Mass: 27073.854 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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: 4.83 Å3/Da / Density % sol: 74.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES (pH 7.0) 15% w/v PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.12→63.43 Å / Num. obs: 308558 / % possible obs: 98.2 % / Redundancy: 9.3 % / Biso Wilson estimate: 93.07 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.088 / Rrim(I) all: 0.167 / Net I/σ(I): 7.6
Reflection shellResolution: 3.12→3.2 Å / Rmerge(I) obs: 1.647 / Num. unique obs: 22927 / CC1/2: 0.34 / Rpim(I) all: 0.994 / Rrim(I) all: 1.927

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Processing

Software
NameVersionClassification
XDS1.20.1_4487data scaling
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→35 Å / SU ML: 0.4146 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.5043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 11413 5 %
Rwork0.2091 216837 -
obs0.2103 228250 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.27 Å2
Refinement stepCycle: LAST / Resolution: 3.45→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms65289 0 0 0 65289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002766993
X-RAY DIFFRACTIONf_angle_d0.548890924
X-RAY DIFFRACTIONf_chiral_restr0.0449452
X-RAY DIFFRACTIONf_plane_restr0.004311991
X-RAY DIFFRACTIONf_dihedral_angle_d15.577524502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.490.38473490.33986628X-RAY DIFFRACTION90.35
3.49-3.530.35363830.29327277X-RAY DIFFRACTION98.62
3.53-3.570.29673850.2877333X-RAY DIFFRACTION98.67
3.57-3.620.29863820.27827246X-RAY DIFFRACTION98.74
3.62-3.660.30293850.28337330X-RAY DIFFRACTION98.56
3.66-3.710.27473810.27247228X-RAY DIFFRACTION98.45
3.71-3.770.29773850.26267316X-RAY DIFFRACTION98.86
3.77-3.820.29663790.26017189X-RAY DIFFRACTION98.81
3.82-3.880.2853840.26097301X-RAY DIFFRACTION98.79
3.88-3.950.28333860.2577324X-RAY DIFFRACTION98.48
3.95-4.010.2883820.25137264X-RAY DIFFRACTION98.93
4.01-4.090.27713840.24427306X-RAY DIFFRACTION98.96
4.09-4.160.29553850.247312X-RAY DIFFRACTION99.02
4.16-4.250.24043860.2257322X-RAY DIFFRACTION99.07
4.25-4.340.2313820.20987267X-RAY DIFFRACTION99.05
4.34-4.440.21363840.19887297X-RAY DIFFRACTION99.14
4.44-4.550.21233850.19897318X-RAY DIFFRACTION99.24
4.55-4.680.21613870.1897345X-RAY DIFFRACTION99.12
4.68-4.810.2073840.18527289X-RAY DIFFRACTION99.17
4.81-4.970.21163850.18657315X-RAY DIFFRACTION99.12
4.97-5.150.21583830.18917281X-RAY DIFFRACTION99.2
5.15-5.350.24513860.19537331X-RAY DIFFRACTION99.06
5.35-5.590.24043850.20227319X-RAY DIFFRACTION98.92
5.59-5.890.23393840.20097301X-RAY DIFFRACTION99.07
5.89-6.250.23613850.20987307X-RAY DIFFRACTION99.12
6.25-6.730.22443840.21117295X-RAY DIFFRACTION99.12
6.73-7.410.22063840.18737295X-RAY DIFFRACTION98.55
7.41-8.460.17393790.16927193X-RAY DIFFRACTION97.87
8.46-10.610.1653670.13956999X-RAY DIFFRACTION94.63
10.61-350.18213330.16546309X-RAY DIFFRACTION85.68

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