6WZY: DbNA(10) peptides

Structure of DbNA(10) peptides bound to H-2Db MHC-I. Determined by X-ray diffraction at 1.5 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Mus musculus, Homo sapiens, Influenza A virus
Chains: 3
Atoms: 3,770
Mol. weight: 45.48 kDa
Ligands: PO4
Released: 16 Sept 2020

Explore 6WZY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WZY contains 14 α-helices and 28 β-strands across 2 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	4-12	9	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
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	140-150	11
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
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	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	36-41	6	6
β-strand	44-45	2	6
α-helix	46	1
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A	protein	279	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Epitope from Neuraminidase Protein (NA-181-190)	C	protein	10	Influenza A virus	P03468 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6WZY_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A)
MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY
WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE
GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPP

Sequence of entity 2 (B), FASTA

>6WZY_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6WZY_3 Epitope from Neuraminidase Protein (NA-181-190) (chains C)
SGPDNGAVAV

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (EDO, PEG) are not listed.

Primary citation

Overlapping Peptides Elicit Distinct CD8 + T Cell Responses following Influenza A Virus Infection. Assmus, L.M., Guan, J., Wu, T. et al. J Immunol (2020) 205:1731-1742. DOI 10.4049/jimmunol.2000689 · PubMed

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

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…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…

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