3E3Q: 3alpham13 high-affinity mutant of the 2C TCR

Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9. Determined by X-ray diffraction at 2.95 Å resolution. Released 4 Nov 2008.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Mus musculus
Chains: 32
Atoms: 25,808
Mol. weight: 365.72 kDa
Released: 4 Nov 2008

Explore 3E3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E3Q contains 80 α-helices and 250 β-strands across 32 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains a, e, E, F, N, S and W: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	31-37	7	15
β-strand	44-49	6	15
β-strand	56-57	2	15
β-strand	65-68	4	14
β-strand	74-79	6	14
α-helix	84-86	3
β-strand	88-95	8	15
β-strand	107-108	2	15
β-strand	112-117	6	15

Chains A and B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10

Chains b, f, K and O: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6

Chains c, H, L, P, U and Y: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	20
α-helix	20	1
β-strand	21-28	8	20
β-strand	31-37	7	20
β-strand	45-47	3	20
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	20
β-strand	109-118	10	20
β-strand	121-126	6	20
β-strand	133-135	3	20
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9

Chains C, d, I, R, V and Z: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	16
β-strand	9-12	4	17
β-strand	18-20	3	16
β-strand	23-24	2	16
β-strand	32-37	6	17
β-strand	44-49	6	17
β-strand	55-58	4	16
β-strand	62-67	6	16
β-strand	72-77	6	16
α-helix	82-84	3
β-strand	86-93	8	17
β-strand	104-106	3	17
β-strand	110-114	5	17

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	6
β-strand	9-12	4	7
β-strand	18-20	3	6
β-strand	23-24	2	6
β-strand	32-37	6	7
β-strand	44-49	6	7
β-strand	55-57	3	6
β-strand	63-67	5	6
β-strand	72-77	6	6
α-helix	82-84	3
β-strand	86-93	8	7
β-strand	104-106	3	7
β-strand	110-114	5	7

Chains G, Q and X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7

Chain J: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-21	3	30
β-strand	22-25	4	28
β-strand	31-37	7	29
β-strand	44-49	6	29
β-strand	56-57	2	29
β-strand	65-68	4	30
β-strand	74	1	28
β-strand	76-79	4	30
α-helix	84-86	3
β-strand	88-95	8	29
β-strand	107-108	2	29
β-strand	112-117	6	29

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, L-D alpha chain	A, B, H, L, P, U, Y, c	protein	175	Mus musculus	P01897 (AlphaFold model)
QL9 peptide	G, K, O, Q, T, X, b, f	protein	9
T-cell receptor alpha chain V region PHDS58	C, D, I, M, R, V, Z, d	protein	109	Mus musculus	P01738 (AlphaFold model)
TCR beta chain	E, F, J, N, S, W, a, e	protein	111	Mus musculus

Sequence of entity 1 (A, B, H, L, P, U, Y, c), FASTA

>3E3Q_1 H-2 class I histocompatibility antigen, L-D alpha chain (chains A, B, H, L, P, U, Y, c)
GPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW
ERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG
CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG

Sequence of entity 2 (G, K, O, Q, T, X, b, f), FASTA

>3E3Q_2 QL9 peptide (chains G, K, O, Q, T, X, b, f)
QLSPFPFDL

Sequence of entity 3 (C, D, I, M, R, V, Z, d), FASTA

>3E3Q_3 T-cell receptor alpha chain V region PHDS58 (chains C, D, I, M, R, V, Z, d)
SVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVNG
FEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSDPPPLLTFGSGTKVIVL

Sequence of entity 4 (E, F, J, N, S, W, a, e), FASTA

>3E3Q_4 TCR beta chain (chains E, F, J, N, S, W, a, e)
EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIYYSYGAGSTEKGDI
PDGYKASRPSQENFSLTLESATPSQTSVYFCASGGGGTLYFGAGTRLSVLS

Primary citation

Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation. Jones, L.L., Colf, L.A., Stone, J.D. et al. J Immunol (2008) 181:6255-6264. PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
8D5N 1.8 Å, Crystal structure of Ld-HF10
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex

Browse structure collections

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