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- PDB-8i5c: 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: 8i5c
TitleCrystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVGAVGVGK)
Components
  • Beta-2-microglobulin
  • MHC class I antigen (Fragment)
  • TCR alpha chain
  • TCR beta chain
  • peptide KRAS-G12V-9
KeywordsIMMUNE SYSTEM / KRAS / TCR
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma 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-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 / : ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsLu, D. / Chen, Y. / Jiang, M. / Tan, S.G. / Chai, Y. / Gao, G.F.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022YFC2302900 China
National Natural Science Foundation of China (NSFC)2021YFC2301400 China
National Natural Science Foundation of China (NSFC)92169208 China
National Natural Science Foundation of China (NSFC)32222031 China
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVGAVGVGK)
Authors: Lu, D. / Chen, Y. / Jiang, M. / Tan, S.G. / Chai, Y. / Gao, G.F.
History
DepositionJan 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.2Oct 16, 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 (Fragment)
B: Beta-2-microglobulin
C: peptide KRAS-G12V-9
D: TCR alpha chain
E: TCR beta chain
F: MHC class I antigen (Fragment)
G: Beta-2-microglobulin
H: peptide KRAS-G12V-9
I: TCR alpha chain
J: TCR beta chain
K: MHC class I antigen (Fragment)
L: Beta-2-microglobulin
M: peptide KRAS-G12V-9
N: TCR alpha chain
O: TCR beta chain
P: MHC class I antigen (Fragment)
Q: Beta-2-microglobulin
R: peptide KRAS-G12V-9
S: TCR alpha chain
T: TCR beta chain
U: MHC class I antigen (Fragment)
V: Beta-2-microglobulin
W: peptide KRAS-G12V-9
X: TCR alpha chain
Y: TCR beta chain
Z: MHC class I antigen (Fragment)
a: Beta-2-microglobulin
b: peptide KRAS-G12V-9
c: TCR alpha chain
d: TCR beta chain
e: MHC class I antigen (Fragment)
f: Beta-2-microglobulin
g: peptide KRAS-G12V-9
h: TCR alpha chain
i: TCR beta chain
j: MHC class I antigen (Fragment)
k: Beta-2-microglobulin
l: peptide KRAS-G12V-9
m: TCR alpha chain
n: TCR beta chain
o: MHC class I antigen (Fragment)
p: Beta-2-microglobulin
q: peptide KRAS-G12V-9
r: TCR alpha chain
s: TCR beta chain
t: MHC class I antigen (Fragment)
u: Beta-2-microglobulin
v: peptide KRAS-G12V-9
w: TCR alpha chain
x: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)937,28850
Polymers937,28850
Non-polymers00
Water00
1
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: peptide KRAS-G12V-9
D: TCR alpha chain
E: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen (Fragment)
G: Beta-2-microglobulin
H: peptide KRAS-G12V-9
I: TCR alpha chain
J: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: MHC class I antigen (Fragment)
L: Beta-2-microglobulin
M: peptide KRAS-G12V-9
N: TCR alpha chain
O: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: MHC class I antigen (Fragment)
Q: Beta-2-microglobulin
R: peptide KRAS-G12V-9
S: TCR alpha chain
T: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
U: MHC class I antigen (Fragment)
V: Beta-2-microglobulin
W: peptide KRAS-G12V-9
X: TCR alpha chain
Y: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
Z: MHC class I antigen (Fragment)
a: Beta-2-microglobulin
b: peptide KRAS-G12V-9
c: TCR alpha chain
d: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
e: MHC class I antigen (Fragment)
f: Beta-2-microglobulin
g: peptide KRAS-G12V-9
h: TCR alpha chain
i: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
j: MHC class I antigen (Fragment)
k: Beta-2-microglobulin
l: peptide KRAS-G12V-9
m: TCR alpha chain
n: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
o: MHC class I antigen (Fragment)
p: Beta-2-microglobulin
q: peptide KRAS-G12V-9
r: TCR alpha chain
s: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
t: MHC class I antigen (Fragment)
u: Beta-2-microglobulin
v: peptide KRAS-G12V-9
w: TCR alpha chain
x: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,7295
Polymers93,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.864, 156.889, 191.966
Angle α, β, γ (deg.)77.370, 78.130, 82.270
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 (Fragment)


Mass: 31753.006 Da / Num. of mol.: 10 / Mutation: A245V,E253Q
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: U5YJJ6
#2: Protein
Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide
peptide KRAS-G12V-9


Mass: 785.951 Da / Num. of mol.: 10 / Mutation: G12V / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein
TCR alpha chain


Mass: 22412.898 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
TCR beta chain


Mass: 27028.770 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: 4.79 Å3/Da / Density % sol: 74.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Ammonium citrate tribasic pH 7.0, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. obs: 249244 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 79.13 Å2 / Rmerge(I) obs: 0.199 / Net I/σ(I): 6.609
Reflection shellResolution: 3.35→3.47 Å / Rmerge(I) obs: 0.814 / Num. unique obs: 24856

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.20.1_4487refinement
Cootmodel building
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UON, 6DFV, 6OVN, 7Z50

6uon

6dfv

6ovn

7z50


Resolution: 3.34→49.82 Å / SU ML: 0.4519 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.9936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 11615 4.98 %
Rwork0.2243 221794 -
obs0.226 233409 92.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.58 Å2
Refinement stepCycle: LAST / Resolution: 3.34→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms65732 0 0 0 65732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001667442
X-RAY DIFFRACTIONf_angle_d0.42891560
X-RAY DIFFRACTIONf_chiral_restr0.04069539
X-RAY DIFFRACTIONf_plane_restr0.003312079
X-RAY DIFFRACTIONf_dihedral_angle_d10.45324686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.380.3761930.33233890X-RAY DIFFRACTION48.72
3.38-3.420.33972720.33435192X-RAY DIFFRACTION64.43
3.42-3.460.37262920.33615501X-RAY DIFFRACTION69.08
3.46-3.50.35633140.30936269X-RAY DIFFRACTION77.75
3.5-3.550.34853550.28446668X-RAY DIFFRACTION83.42
3.55-3.60.33483390.28586896X-RAY DIFFRACTION86.3
3.6-3.650.32223720.29547133X-RAY DIFFRACTION88.44
3.65-3.70.36073210.31787290X-RAY DIFFRACTION91.17
3.7-3.760.33443800.28727817X-RAY DIFFRACTION96.75
3.76-3.820.334390.27947942X-RAY DIFFRACTION98.2
3.82-3.890.33194310.28777726X-RAY DIFFRACTION98.35
3.89-3.960.31254370.2877813X-RAY DIFFRACTION97.7
3.96-4.030.28113820.25437982X-RAY DIFFRACTION98.75
4.03-4.120.27674030.24837907X-RAY DIFFRACTION98.87
4.12-4.20.28223850.23937930X-RAY DIFFRACTION98.84
4.2-4.30.25274420.22547928X-RAY DIFFRACTION99.03
4.3-4.410.22954110.19697923X-RAY DIFFRACTION98.99
4.41-4.530.21374130.1967954X-RAY DIFFRACTION99.14
4.53-4.660.21724270.18697911X-RAY DIFFRACTION99.19
4.66-4.810.23014740.19627942X-RAY DIFFRACTION99.32
4.81-4.980.24143890.19277707X-RAY DIFFRACTION96.37
4.98-5.180.2344420.19337740X-RAY DIFFRACTION96.82
5.18-5.420.22444570.20327918X-RAY DIFFRACTION99.23
5.42-5.710.23663630.20687954X-RAY DIFFRACTION99.18
5.71-6.060.23574080.20528001X-RAY DIFFRACTION99.17
6.06-6.530.26364250.22547935X-RAY DIFFRACTION99.23
6.53-7.180.25984450.20757932X-RAY DIFFRACTION99.36
7.18-8.220.2213630.18928029X-RAY DIFFRACTION99.54
8.22-10.340.17994380.167936X-RAY DIFFRACTION99.42
10.34-49.820.22134030.18917028X-RAY DIFFRACTION88.21

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