8I5C | pdb_00008i5c

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

PDB DOI: https://doi.org/10.2210/pdb8I5C/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-01-24 Released: 2023-08-23
Deposition Author(s): Lu, D., Chen, Y., Jiang, M., Tan, S.G., Chai, Y., Gao, G.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.34 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.224 (Depositor), 0.230 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

Lu, D., Chen, Y., Jiang, M., Tan, S.G., Chai, Y., Gao, G.F.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 937.29 kDa
Atom Count: 65,732
Modeled Residue Count: 8,199
Deposited Residue Count: 8,230
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen (Fragment)	A EA [auth e] F JA [auth j] K A, EA [auth e], F, JA [auth j], K, OA [auth o], P, TA [auth t], U, Z	274	Homo sapiens	Mutation(s): 2 Gene Names: HLA-A
UniProt
Find proteins for U5YJJ6 (Homo sapiens) Explore U5YJJ6 Go to UniProtKB: U5YJJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5YJJ6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	AA [auth a] B FA [auth f] G KA [auth k] AA [auth a], B, FA [auth f], G, KA [auth k], L, PA [auth p], Q, UA [auth u], V	99	Homo sapiens	Mutation(s): 0 Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide KRAS-G12V-9	BA [auth b] C GA [auth g] H LA [auth l] BA [auth b], C, GA [auth g], H, LA [auth l], M, QA [auth q], R, VA [auth v], W	9	Homo sapiens	Mutation(s): 0 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR alpha chain	CA [auth c] D HA [auth h] I MA [auth m] CA [auth c], D, HA [auth h], I, MA [auth m], N, RA [auth r], S, WA [auth w], X	199	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR beta chain	DA [auth d] E IA [auth i] J NA [auth n] DA [auth d], E, IA [auth i], J, NA [auth n], O, SA [auth s], T, XA [auth x], Y	242	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.34 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.224 (Depositor), 0.230 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.864	α = 77.37
b = 156.889	β = 78.13
c = 191.966	γ = 82.27

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2022YFC2302900
National Natural Science Foundation of China (NSFC)	China	2021YFC2301400
National Natural Science Foundation of China (NSFC)	China	92169208
National Natural Science Foundation of China (NSFC)	China	32222031