5WKF: D30 TCR

D30 TCR in complex with HLA-A*11:01-GTS1. Determined by X-ray diffraction at 2.95 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Homo sapiens, Dengue virus 1
Chains: 10
Atoms: 13,580
Mol. weight: 187.78 kDa
Released: 20 Sept 2017

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

Secondary structure: helices and β-sheets

5WKF contains 48 α-helices and 153 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: 7 helices, 19 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	57-84	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	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-223	2	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-263	7	4
β-strand	270-273	4	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chains C and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	8

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	9
β-strand	10-14	5	10
β-strand	19-24	6	9
β-strand	32-37	6	10
α-helix	41-43	3
β-strand	44-49	6	10
β-strand	50	1	11
β-strand	53	1	11
β-strand	55-58	4	9
β-strand	61-66	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	86-91	6	10
β-strand	100	1	10
β-strand	104-109	6	10
β-strand	118-122	5	12
β-strand	123-124	2	13
β-strand	132-136	5	12
α-helix	143-147	5
β-strand	152-154	3	12
α-helix	155-157	3
β-strand	158-161	4	12
β-strand	168-176	9	12
β-strand	197	1	12

Chain E: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	14
β-strand	10-14	5	15
β-strand	19-24	6	14
β-strand	31-44	7	15
α-helix	49-50	2
β-strand	51-57	7	15
β-strand	60-67	4	15
β-strand	76-79	4	14
β-strand	87-91	5	14
α-helix	94-95	2
α-helix	96-98	3
β-strand	101-107	7	15
β-strand	113	1	8
α-helix	117-119	3
β-strand	120-121	2	15
β-strand	125-130	6	15
α-helix	133-135	3
β-strand	137	1	16
β-strand	140-145	6	13
α-helix	146-147	2
α-helix	148-153	6
β-strand	156-166	11	13
β-strand	167	1	16
β-strand	171-177	7	17
β-strand	180-182	3	17
β-strand	186-188	3	13
α-helix	192	1
β-strand	193-194	2	13
α-helix	202-203	2
β-strand	204-213	10	13
α-helix	214-218	5
β-strand	223-230	8	17
β-strand	233	1	18
α-helix	244-245	2
β-strand	247	1	18
β-strand	249-256	8	17

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	19
α-helix	20	1
β-strand	21-28	8	19
β-strand	31-37	7	19
β-strand	46-47	2	19
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	19
β-strand	109-118	10	19
β-strand	121-126	6	19
β-strand	133-135	3	19
α-helix	140-149	10
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
β-strand	183	1	20
β-strand	186-193	8	21
β-strand	198-208	11	21
β-strand	209	1	20
β-strand	213-219	7	22
β-strand	222-223	2	22
β-strand	229-230	2	21
α-helix	231-233	3
β-strand	234-235	2	21
β-strand	241-250	10	21
β-strand	257-263	7	22
β-strand	270-272	3	22

Chain G: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	23
α-helix	4-5	2
β-strand	6	1	24
β-strand	9-11	3	24
β-strand	21-30	10	24
β-strand	31	1	23
β-strand	36-41	6	25
β-strand	45	1	25
β-strand	50-51	2	24
α-helix	52-54	3
β-strand	55-56	2	24
β-strand	62-70	9	24
β-strand	78-83	6	25
β-strand	91-94	4	25

Chain I: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	27
β-strand	10-14	5	28
β-strand	19-24	6	27
β-strand	33-44	7	28
α-helix	49-50	2
β-strand	51-56	6	28
β-strand	57	1	29
β-strand	60	1	29
β-strand	66-69	4	27
β-strand	72-77	6	27
β-strand	82-87	6	27
α-helix	92-94	3
β-strand	96-103	8	28
β-strand	110-112	3	28
β-strand	116-121	6	28
α-helix	122-123	2
β-strand	130-134	5	30
β-strand	136	1	31
β-strand	144-150	7	30
α-helix	155-159	5
β-strand	164-166	3	30
α-helix	167-169	3
β-strand	170-171	2	30
β-strand	182-188	7	30
β-strand	209	1	30

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)
GTS1 peptide	C, H	protein	10	Dengue virus 1	P17763 (AlphaFold model)
T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain Chimera	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

>5WKF_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

>5WKF_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5WKF_3 GTS1 peptide (chains C, H)
GTSGSPIVNR

Sequence of entity 4 (D, I), FASTA

>5WKF_4 T-cell receptor alpha variable 30,T-cell receptor, sp3.4 alpha chain Chimera (chains D, I)
QPVQSPQAVILREGEDAIINCSSSKALYSVHWYRQKHGEAPIFLMILLKGGEQKGHDKIS
ASFNEKKQQSSLYLTASQLSYSGTYFCGLGDAGNMLTFGGGTRLMVKPHIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPS

Sequence of entity 5 (E, J), FASTA

>5WKF_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

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