2ESV: HLA-E-VMAPRTLIL/KK50.4 TCR complex

Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 21 Mar 2006.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,777
Mol. weight: 94.9 kDa
Released: 21 Mar 2006

Explore 2ESV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ESV contains 27 α-helices and 70 β-strands across 4 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.

Chain A: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-140	3
α-helix	141-149	9
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-217	4	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	259-262	4	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	8
β-strand	8-12	5	9
β-strand	17-22	6	8
β-strand	30-36	8	9
β-strand	43-48	6	9
β-strand	54-55	2	8
β-strand	62-65	4	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-93	9	9
β-strand	109-114	6	9
β-strand	123-127	5	10
β-strand	128-129	2	11
β-strand	137-141	5	10
α-helix	150-152	3
β-strand	158-159	2	10
α-helix	160-162	3
β-strand	163-167	5	10
α-helix	168-170	3
β-strand	172-180	9	10
α-helix	197-198	2
β-strand	202	1	10

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	9
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	31-38	8	9
β-strand	43-50	8	9
β-strand	53-56	4	9
β-strand	65-68	4	12
β-strand	75-79	5	12
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	107-108	2	9
β-strand	112-117	6	9
α-helix	120-122	3
β-strand	124	1	13
α-helix	125-126	2
β-strand	127-132	6	11
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	11
β-strand	154	1	13
β-strand	158-164	7	14
β-strand	167-169	3	14
β-strand	173-175	3	11
α-helix	179	1
β-strand	180-181	2	11
β-strand	191-200	10	11
α-helix	201-204	4
β-strand	210-217	8	14
β-strand	220	1	15
α-helix	231-232	2
β-strand	234	1	15
β-strand	236-243	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A	protein	275	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
VMAPRTLIL peptide from CMV gpUL40	P	protein	9		P16780
KK50.4 T cell receptor alpha chain	D	protein	199	Homo sapiens	P01848 (AlphaFold model)
KK50.4 T cell receptor beta chain	E	protein	240	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>2ESV_1 HLA class I histocompatibility antigen, alpha chain E (chains A)
SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWD
RETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDRRFLRGYEQFAYDGK
DYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH
LEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B), FASTA

>2ESV_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P), FASTA

>2ESV_3 VMAPRTLIL peptide from CMV gpUL40 (chains P)
VMAPRTLIL

Sequence of entity 4 (D), FASTA

>2ESV_4 KK50.4 T cell receptor alpha chain (chains D)
KTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMASL
IITEDRKSSTLILPHATLRDTAVYYCIVVRSSNTGKLIFGQGTTLQVKPDIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>2ESV_5 KK50.4 T cell receptor beta chain (chains E)
GVTQFPSHSVIEKGQTVTLRCDPISGHDNLYWYRRVMGKEIKFLLHFVKESKQDESGMPN
NRFLAERTGGTYSTLKVQPAELEDSGVYFCASSQDRDTQYFGPGTRLTVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

Structural basis for a major histocompatibility complex class Ib-restricted T cell response. Hoare, H.L., Sullivan, L.C., Pietra, G. et al. Nat Immunol (2006) 7:256-264. DOI 10.1038/ni1312 · PubMed

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV

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