5WJL: HLA-A*11:01 with GTS1 peptide

Crystal Structure of HLA-A*11:01 with GTS1 peptide. Determined by X-ray diffraction at 3.15 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, Dengue virus 1
Chains: 9
Atoms: 9,520
Mol. weight: 133.89 kDa
Released: 20 Sept 2017

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

Secondary structure: helices and β-sheets

5WJL contains 33 α-helices and 94 β-strands across 6 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, 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
α-helix	45	1
β-strand	46-47	2	1
α-helix	50-53	4
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	138-150	13
α-helix	152-157	6
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-192	7	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-224	3	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	253-256	4
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	9-11	3	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	91-92	2	7

Chain D: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-54	5
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
β-strand	257-262	6	11
β-strand	271-273	3	11

Chain E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6	1	13
β-strand	9-11	3	14
β-strand	21-30	10	14
β-strand	31	1	12
β-strand	35-41	7	15
β-strand	44-45	2	15
β-strand	50-51	2	14
α-helix	52-54	3
β-strand	55-56	2	14
β-strand	62-70	9	14
β-strand	78-84	7	15
β-strand	91-94	4	15

Chain G: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	16
β-strand	21-28	8	16
β-strand	31-37	7	16
β-strand	46-47	2	16
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	16
β-strand	109-118	10	16
β-strand	121-126	6	16
β-strand	133-135	3	16
α-helix	139-149	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	17
β-strand	188-195	8	18
β-strand	198-208	11	18
β-strand	209	1	17
β-strand	214-219	6	19
β-strand	222-223	2	19
β-strand	228-230	3	18
α-helix	231-233	3
β-strand	234-235	2	18
β-strand	241-250	10	18
α-helix	253-256	4
β-strand	257-262	6	19
β-strand	272-273	2	19

Chain H: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	6	1	21
β-strand	9-11	3	22
α-helix	14-15	2
β-strand	21-27	7	22
β-strand	28	1	21
β-strand	31	1	20
β-strand	36-41	6	23
β-strand	44-45	2	23
α-helix	46	1
β-strand	50-51	2	22
β-strand	55-56	2	24
β-strand	62-63	2	24
β-strand	64-70	7	22
β-strand	78-83	6	23
β-strand	91-94	4	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-11 alpha chain	A, D, G	protein	274	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, E, H	protein	100	Homo sapiens	P61769 (AlphaFold model)
GTS1 peptide	C, F, I	protein	10	Dengue virus 1	P17763 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>5WJL_1 HLA class I histocompatibility antigen, A-11 alpha chain (chains A, D, G)
GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B, E, H), FASTA

>5WJL_2 Beta-2-microglobulin (chains B, E, H)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, I), FASTA

>5WJL_3 GTS1 peptide (chains C, F, I)
GTSGSPIVNR

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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