7N5Q: PDB entry 7N5Q

Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation. Determined by X-ray diffraction at 1.76 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 1.76 Å
Organisms: Mus musculus, Homo sapiens, Influenza A virus
Chains: 6
Atoms: 7,029
Mol. weight: 91.75 kDa
Released: 20 Jul 2022

Explore 7N5Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N5Q contains 29 α-helices and 58 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	19-20	2
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	93-103	11	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	152-158	7
α-helix	159-164	6
α-helix	165-179	15
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	224	1
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4
α-helix	276-278	3

Chain B: 3 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
α-helix	46	1
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	2-6	5

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	8
α-helix	18-20	3
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	57-84	28
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	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	9
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-218	5	11
β-strand	223	1	11
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	258-262	5	11
β-strand	270-272	3	11

Chain G: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-11	6	12
β-strand	21-30	10	12
β-strand	36-41	6	13
β-strand	44-45	2	13
β-strand	50-51	2	12
α-helix	52-54	3
β-strand	55-56	2	12
β-strand	62-70	9	12
β-strand	78-83	6	13
β-strand	91-94	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, F	protein	281	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
peptide from Polymerase acidic protein	C, H	protein	10	Influenza A virus	O89752

Sequence of entity 1 (A, F), FASTA

>7N5Q_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, F)
MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEY
WERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYE
GRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATL
LRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDG
TFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPSTD

Sequence of entity 2 (B, G), FASTA

>7N5Q_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>7N5Q_3 peptide from Polymerase acidic protein (chains C, H)
SSLCNFRAYV

Primary citation

Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Szeto, C., Zareie, P., Wirasinha, R.C. et al. Nat Commun (2022) 13:4951-4951. DOI 10.1038/s41467-022-32692-4 · 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
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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