5WLG: H-2Db with the GAP501 peptide

Crystal Structure of H-2Db with the GAP501 peptide (SQL). Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Mus musculus, Plasmodium berghei, Homo sapiens
Chains: 10
Atoms: 13,901
Mol. weight: 185.1 kDa
Released: 15 Nov 2017

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

Secondary structure: helices and β-sheets

5WLG contains 42 α-helices and 146 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	4-12	9	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	138-150	13
α-helix	153-161	9
α-helix	163-174	12
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-218	5	4
β-strand	222	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	258-262	5	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
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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	8
β-strand	18-23	6	9
β-strand	30-36	7	8
β-strand	43-49	7	8
β-strand	54-57	4	9
β-strand	60-65	6	9
α-helix	66-68	3
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	84-91	8	8
β-strand	96-98	3	8
α-helix	99-101	3
β-strand	102-107	6	8
β-strand	116-121	6	10
β-strand	122	1	11
β-strand	129-134	6	10
α-helix	140-142	3
β-strand	150-152	3	10
α-helix	153-155	3
β-strand	156-160	5	10
β-strand	165-174	10	10
α-helix	181-184	4

Chain E: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-24	3	12
β-strand	31-37	7	13
β-strand	43-49	7	13
β-strand	56-57	2	13
β-strand	65-67	3	14
β-strand	73	1	12
β-strand	75-78	4	14
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	103-104	2	13
β-strand	108-113	6	13
α-helix	116-118	3
β-strand	120	1	15
α-helix	121-122	2
β-strand	123-127	5	11
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	11
β-strand	150	1	15
β-strand	154-160	7	16
β-strand	163-165	3	16
β-strand	169-171	3	11
β-strand	176-177	2	11
β-strand	182	1	17
β-strand	187-196	10	11
α-helix	197-200	4
β-strand	206-213	8	16
β-strand	216	1	18
α-helix	227-228	2
β-strand	230	1	18
β-strand	232-239	8	16

Chain F: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	19
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	138-150	13
α-helix	153-161	9
α-helix	163-174	12
β-strand	183	1	20
β-strand	186-193	8	21
β-strand	199-208	10	21
β-strand	209	1	20
β-strand	214-219	6	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	241-249	9	21
α-helix	254-256	3
β-strand	257-262	6	22
β-strand	270-272	3	22

Chain G: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	23
α-helix	4-5	2
β-strand	6-11	6	24
β-strand	21-30	10	24
β-strand	31	1	23
β-strand	36-41	6	25
β-strand	44-45	2	25
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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	26
β-strand	18-23	6	27
β-strand	30-36	7	26
β-strand	43-49	7	26
β-strand	55-58	4	27
β-strand	61-66	6	27
β-strand	71-76	6	27
α-helix	81-83	3
β-strand	85-92	8	26
β-strand	97-99	3	26
α-helix	100-102	3
β-strand	103-108	6	26
β-strand	117-121	5	28
β-strand	123	1	29
β-strand	131-135	5	28
α-helix	141-146	6
β-strand	151-153	3	28
α-helix	154-156	3
β-strand	157-161	5	28
β-strand	166-175	10	28

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
H-2 class I histocompatibility antigen, D-B alpha chain	A, F	protein	278	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	99	Mus musculus	P01887 (AlphaFold model)
GAP50 peptide	C, H	protein	9	Plasmodium berghei	A0A0Y9W4B5 (AlphaFold model)
T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain	D, I	protein	182	Mus musculus, Homo sapiens	K7N5M3 (AlphaFold model)
T-cell receptor beta chain V region C5,Human nkt tcr beta chain	E, J	protein	243	Mus musculus, Homo sapiens	K7N5M4, P04213

Sequence of entity 1 (A, F), FASTA

>5WLG_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, F)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPP

Sequence of entity 2 (B, G), FASTA

>5WLG_2 Beta-2-microglobulin (chains B, G)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (C, H), FASTA

>5WLG_3 GAP50 peptide (chains C, H)
SQLLNAKYL

Sequence of entity 4 (D, I), FASTA

>5WLG_4 T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain (chains D, I)
ENLQALSIQEGEDVTMNCSYKTYTTVVHWYRQDSGRGPALIILIRSNEREKRSGRLRATL
DTSSQSSSLSITAAQCEDTAVYFCATVYAQGLTFGLGTRVSVFPNIQNPDPAVYQLRDSK
SSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANA
FN

Sequence of entity 5 (E, J), FASTA

>5WLG_5 T-cell receptor beta chain V region C5,Human nkt tcr beta chain (chains E, J)
EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDI
PDGYKASRPSQENFSLILELASLSQTAVYFCASSDWGDTGQLYFGEGSKLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene. Van Braeckel-Budimir, N., Gras, S., Ladell, K. et al. Immunity (2017) 47:835-847.e4. DOI 10.1016/j.immuni.2017.10.013 · PubMed

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

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