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Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVGAVGVGK)

X-ray diffraction
3.34Å resolution
PDB entry 8i5c coloured by chain, front view.
PDB entry 8i5c coloured by chain, side view.
PDB entry 8i5c coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 37868.98 Å2
Buried surface area: 10459.39 Å2
Dissociation area: 1,114.82 Å2
Dissociation energy (ΔGdiss): -6.24 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 10
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Multimeric state: hetero pentamer
Accessible surface area: 38072.32 Å2
Buried surface area: 10135.45 Å2
Dissociation area: 1,134.14 Å2
Dissociation energy (ΔGdiss): -6.06 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 2
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Multimeric state: hetero pentamer
Accessible surface area: 37977.12 Å2
Buried surface area: 10396.37 Å2
Dissociation area: 1,074.97 Å2
Dissociation energy (ΔGdiss): -7.19 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 3
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Multimeric state: hetero pentamer
Accessible surface area: 37961.44 Å2
Buried surface area: 10402.62 Å2
Dissociation area: 1,097.87 Å2
Dissociation energy (ΔGdiss): -6.41 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 4
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Multimeric state: hetero pentamer
Accessible surface area: 37938.18 Å2
Buried surface area: 10401.96 Å2
Dissociation area: 1,110.73 Å2
Dissociation energy (ΔGdiss): -6.59 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 5
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Multimeric state: hetero pentamer
Accessible surface area: 37960.13 Å2
Buried surface area: 10447.44 Å2
Dissociation area: 1,122.04 Å2
Dissociation energy (ΔGdiss): -6.31 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 6
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Multimeric state: hetero pentamer
Accessible surface area: 38122.93 Å2
Buried surface area: 10403.06 Å2
Dissociation area: 1,136.39 Å2
Dissociation energy (ΔGdiss): -4.44 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 7
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Multimeric state: hetero pentamer
Accessible surface area: 37931.56 Å2
Buried surface area: 10499.11 Å2
Dissociation area: 1,121.63 Å2
Dissociation energy (ΔGdiss): -6.82 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 8
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Multimeric state: hetero pentamer
Accessible surface area: 37965.43 Å2
Buried surface area: 10495.26 Å2
Dissociation area: 1,147.02 Å2
Dissociation energy (ΔGdiss): -5.95 kcal/mol
Dissociation entropy (TΔSdiss): 13.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414
Assembly 9
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Multimeric state: hetero pentamer
Accessible surface area: 37912.76 Å2
Buried surface area: 10378.33 Å2
Dissociation area: 1,123.78 Å2
Dissociation energy (ΔGdiss): -4.35 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279414

Macromolecules

Ig-like domain-containing protein
Chains: A, F, K, P, U, Z, e, j, o, t
Length: 274 amino acids
Theoretical weight: 31.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: U5YJJ6 (Residues: 25-298; Coverage: 88%)
Gene name: HLA-A
Pfam:
MHC class I antigen (Fragment) in PDB entry 8i5c, assembly 1, front view.
MHC class I antigen (Fragment) in PDB entry 8i5c, assembly 1, side view.
MHC class I antigen (Fragment) in PDB entry 8i5c, assembly 1, top view.
PDBe-KB: UniProt Coverage View: U5YJJ6  
127420406080100120140160180200220240260
 
100200GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRW
UniProt
U5YJJ6
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
Molecule details ›

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Beta-2-microglobulin
Chains: B, G, L, Q, V, a, f, k, p, u
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Pfam: Immunoglobulin C1-set domain
Beta-2-microglobulin in PDB entry 8i5c, assembly 1, front view.
Beta-2-microglobulin in PDB entry 8i5c, assembly 1, side view.
Beta-2-microglobulin in PDB entry 8i5c, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P61769  
199102030405060708090
 
50100IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
UniProt
P61769
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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GTPase KRas, N-terminally processed
Chains: C, H, M, R, W, b, g, l, q, v
Length: 9 amino acids
Theoretical weight: 786 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01116 (Residues: 8-16; Coverage: 5%)
Gene names: KRAS, KRAS2, RASK2
peptide KRAS-G12V-9 in PDB entry 8i5c, assembly 1, front view.
peptide KRAS-G12V-9 in PDB entry 8i5c, assembly 1, side view.
peptide KRAS-G12V-9 in PDB entry 8i5c, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P01116  
19123456789
 
246810VVGAVGVGK
UniProt
P01116
Chains
Interaction interfaces
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TCR alpha chain
Chains: D, I, N, S, X, c, h, m, r, w
Length: 199 amino acids
Theoretical weight: 22.41 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
TCR alpha chain in PDB entry 8i5c, assembly 1, front view.
TCR alpha chain in PDB entry 8i5c, assembly 1, side view.
TCR alpha chain in PDB entry 8i5c, assembly 1, top view.
119920406080100120140160180
 
50100150200QQKVQQSPESLIVPEGGMASLNCTSSDRNVDYFWWYRQHSGKSPKMLMSIFSNGEKEEGRFTVHLNKASLHTSLHIRDSQPSDSALYLCAARDSNYQLIWGSGTKLIIKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP
Chains
RSRZ Outlier Chain CA (auth c)
Chain CA (auth c)
RSRZ Outlier Chain D (auth D)
Chain D (auth D)
RSRZ Outlier Chain HA (auth h)
Chain HA (auth h)
RSRZ Outlier Chain I (auth I)
Chain I (auth I)
RSRZ Outlier Chain MA (auth m)
Chain MA (auth m)
RSRZ Outlier Chain N (auth N)
Chain N (auth N)
RSRZ Outlier Chain RA (auth r)
Chain RA (auth r)
RSRZ Outlier Chain S (auth S)
Chain S (auth S)
RSRZ Outlier Chain WA (auth w)
Chain WA (auth w)
RSRZ Outlier Chain X (auth X)
Chain X (auth X)
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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TCR beta chain
Chains: E, J, O, T, Y, d, i, n, s, x
Length: 242 amino acids
Theoretical weight: 27.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
TCR beta chain in PDB entry 8i5c, assembly 1, front view.
TCR beta chain in PDB entry 8i5c, assembly 1, side view.
TCR beta chain in PDB entry 8i5c, assembly 1, top view.
124220406080100120140160180200220240
 
100200EAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDTGGYEQYFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD
Chains
RSRZ Outlier Chain DA (auth d)
Chain DA (auth d)
RSRZ Outlier Chain E (auth E)
Chain E (auth E)
RSRZ Outlier Chain IA (auth i)
Chain IA (auth i)
RSRZ Outlier Chain J (auth J)
Chain J (auth J)
RSRZ Outlier Chain NA (auth n)
Chain NA (auth n)
RSRZ Outlier Chain O (auth O)
Chain O (auth O)
RSRZ Outlier Chain SA (auth s)
Chain SA (auth s)
RSRZ Outlier Chain T (auth T)
Chain T (auth T)
RSRZ Outlier Chain XA (auth x)
Chain XA (auth x)
RSRZ Outlier Chain Y (auth Y)
Chain Y (auth Y)
Secondary structure
Interaction interfaces
Sequence conservation
Molecule details ›

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