5WKH: D30 TCR

D30 TCR in complex with HLA-A*11:01-GTS3. Determined by X-ray diffraction at 3.2 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Dengue virus 3
Chains: 10
Atoms: 13,218
Mol. weight: 187.78 kDa
Released: 20 Sept 2017

Explore 5WKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WKH contains 48 α-helices and 150 β-strands across 10 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: 9 helices, 17 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	57-84	28
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	138-148	11
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	183-185	3
β-strand	186-193	8	2
β-strand	198-208	11	2
β-strand	214-219	6	3
β-strand	222-223	2	3
β-strand	228-230	3	2
β-strand	234-235	2	2
β-strand	241-250	10	2
α-helix	254-256	3
β-strand	257-262	6	3
β-strand	270-272	3	3

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-5	2
β-strand	6	1	5
α-helix	7	1
β-strand	9-11	3	5
β-strand	21-30	10	5
β-strand	31	1	4
β-strand	36-41	6	6
β-strand	44-45	2	6
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	6
β-strand	91-94	4	6
α-helix	95-96	2

Chains C and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	7

Chain D: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	10-14	5	9
β-strand	19-24	6	8
α-helix	28-29	2
β-strand	39-44	6	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	57	1	10
β-strand	60	1	10
β-strand	66-69	4	8
β-strand	72-77	6	8
β-strand	82-87	6	8
β-strand	96-102	7	9
β-strand	112	1	9
β-strand	116-121	6	9
β-strand	130-134	5	11
β-strand	144-148	5	11
α-helix	157-159	3
β-strand	164-174	11	11
β-strand	179-188	10	11
β-strand	209	1	11

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	31-44	7	13
α-helix	49-50	2
β-strand	51-57	7	13
β-strand	60-67	4	13
β-strand	76-79	4	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	113	1	7
α-helix	117-119	3
β-strand	120-121	2	13
β-strand	125-130	6	13
α-helix	133-135	3
β-strand	137	1	14
β-strand	140-144	5	15
α-helix	145-147	3
α-helix	148-153	6
β-strand	156-166	11	15
β-strand	167	1	14
β-strand	171-177	7	16
β-strand	180-182	3	16
β-strand	186-188	3	15
β-strand	193-194	2	15
α-helix	202-203	2
β-strand	204-213	10	15
α-helix	214-217	4
β-strand	223-230	8	16
β-strand	233	1	17
β-strand	247	1	17
β-strand	249-256	8	16

Chain F: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
β-strand	21-28	8	18
β-strand	31-37	7	18
α-helix	45	1
β-strand	46-47	2	18
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-115	7	18
β-strand	118	1	18
β-strand	124-126	3	18
β-strand	133-135	3	18
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	19
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	222-223	2	21
β-strand	229-230	2	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	253-256	4
β-strand	257-262	6	21
β-strand	270-272	3	21

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
β-strand	9-11	3	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	44-45	2	24
α-helix	46	1
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
α-helix	90	1
β-strand	91-94	4	24
α-helix	95-96	2

Chain I: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	26
β-strand	10-14	5	27
β-strand	19-24	6	26
β-strand	39-45	7	27
β-strand	48-56	9	27
β-strand	57	1	28
β-strand	60	1	28
β-strand	66-69	4	26
β-strand	72-77	6	26
β-strand	82-87	6	26
α-helix	92-94	3
β-strand	96-103	8	27
β-strand	110-112	3	27
β-strand	116-121	6	27
β-strand	130-134	5	29
β-strand	135-136	2	30
β-strand	143-150	8	29
β-strand	165-166	2	29
α-helix	167-169	3
β-strand	170-171	2	29
β-strand	182-188	7	29
β-strand	209	1	29

1 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
HLA class I histocompatibility antigen, A-11 alpha chain	A, F	protein	274	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
GTS3 peptide	C, H	protein	10	Dengue virus 3	Q6YMS4
T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain	D, I	protein	198	Homo sapiens	A0A087WSZ9 (AlphaFold model), K7N5N2
D30 TCR beta chain	E, J	protein	244	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>5WKH_1 HLA class I histocompatibility antigen, A-11 alpha chain (chains A, F)
GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B, G), FASTA

>5WKH_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5WKH_3 GTS3 peptide (chains C, H)
GTSGSPIINR

Sequence of entity 4 (D, I), FASTA

>5WKH_4 T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain (chains D, I)
QPVQSPQAVILREGEDAVINCSSSKALYSVHWYRQKHGEAPIFLMILLKGGEQKGHDKIS
ASFNEKKQQSSLYLTASQLSYSGTYFCGLGDAGNMLTFGGGTRLMVKPHIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPS

Sequence of entity 5 (E, J), FASTA

>5WKH_5 D30 TCR beta chain (chains E, J)
AGVAQSPRYKIIEKRQSVAFWCNPISGHATLYWYQQILGQGPKLLIQFQNNGVVDDSQLP
KDRFSAERLKGVDSTLKIQPAKLEDSAVYLCASSLGQGLLYGYTFGSGTRLTVLEDLNKV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8(+) T cell response. Culshaw, A., Ladell, K., Gras, S. et al. Nat Immunol (2017) 18:1228-1237. DOI 10.1038/ni.3850 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

Browse structure collections

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