8D5N: Ld-HF10

Crystal structure of Ld-HF10. Determined by X-ray diffraction at 1.8 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Mus musculus, Toxoplasma gondii
Chains: 6
Atoms: 6,715
Mol. weight: 92.73 kDa
Ligands: PPI, NAG
Released: 14 Sept 2022

Explore 8D5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D5N contains 28 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	5
α-helix	20	1
β-strand	21-28	8	5
β-strand	31-37	7	5
β-strand	46-47	2	5
α-helix	50-52	3
α-helix	57-84	28
α-helix	87-88	2
β-strand	94-103	10	5
β-strand	109-118	10	5
β-strand	121-126	6	5
β-strand	133-135	3	5
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	6
α-helix	184-185	2
β-strand	186-195	10	7
β-strand	198-208	11	7
β-strand	209	1	6
β-strand	214-219	6	8
β-strand	222-223	2	8
β-strand	229-230	2	7
α-helix	231-233	3
β-strand	234-235	2	7
β-strand	241-250	10	7
α-helix	254-256	3
β-strand	257-262	6	8
β-strand	270-272	3	8

Chains B and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Chain C: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
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	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-217	4	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	259-262	4	4
β-strand	270-272	3	4

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
α-helix	4-5	2
β-strand	6-11	6	10
β-strand	21-30	10	10
β-strand	31	1	9
β-strand	36-41	6	11
β-strand	44-45	2	11
α-helix	46	1
β-strand	50-51	2	10
β-strand	55-56	2	10
β-strand	62-70	9	10
β-strand	78-83	6	11
α-helix	90	1
β-strand	91-94	4	11

Chain H: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-56	7	13
β-strand	62-70	9	13
β-strand	78-83	6	14
α-helix	90	1
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, L-D alpha chain	A, C	protein	282	Mus musculus	P01897 (AlphaFold model)
Dense granule protein 6, HF10 peptide	B, E	protein	16	Toxoplasma gondii
Beta-2-microglobulin	F, H	protein	104	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8D5N_1 H-2 class I histocompatibility antigen, L-D alpha chain (chains A, C)
GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYW
ERITQIAKGQEQWFRVNLRTLLGCYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDG
SDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWQSTRGGAS

Sequence of entity 2 (B, E), FASTA

>8D5N_2 Dense granule protein 6, HF10 peptide (chains B, E)
HPGSVNEFDFGCGGSG

Sequence of entity 3 (F, H), FASTA

>8D5N_3 Beta-2-microglobulin (chains F, H)
GGSGGIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMS
FSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Ligands and cofactors

ID	Name	Formula	Copies
PPI	Propanoic acid	C3 H6 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (EDO, PG4) are not listed.

Primary citation

Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response. Wang, Y., Tsitsiklis, A., Devoe, S. et al. Front Immunol (2022) 13:847092-847092. DOI 10.3389/fimmu.2022.847092 · PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex
6L9L 2.4 Å, 1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes

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