6NPR: H-2Dd with C84-C139 disulfide

Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide P18-I10. Determined by X-ray diffraction at 2.37 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 2.37 Å
Organisms: Mus musculus, Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 6,482
Mol. weight: 90.09 kDa
Released: 22 Jan 2020

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

Secondary structure: helices and β-sheets

6NPR contains 27 α-helices and 60 β-strands across 4 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	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
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	225-227	3
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

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain C: 11 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	51-54	4
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	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	199-208	10	10
β-strand	209	1	9
β-strand	213-219	7	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-249	9	10
α-helix	254-256	3
β-strand	257-263	7	11
β-strand	270-272	3	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	5
α-helix	5-6	2
β-strand	7-12	6	12
β-strand	22-31	10	12
β-strand	32	1	5
β-strand	37-42	6	13
β-strand	45-46	2	13
β-strand	51-52	2	12
α-helix	53-55	3
β-strand	56-57	2	12
β-strand	63-71	9	12
β-strand	79-84	6	13
β-strand	92-95	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, C	protein	276	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-gly-pro-gly-arg-ala-phe-val-thr-ile	P, R	protein	10	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6NPR_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, C)
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
RETRRAKGNEQSFRVDLRTALRCYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGS
DYIALNEDLKTWTAADMCAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

Sequence of entity 2 (B, D), FASTA

>6NPR_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P, R), FASTA

>6NPR_3 ARG-GLY-PRO-GLY-ARG-ALA-PHE-VAL-THR-ILE (chains P, R)
RGPGRAFVTI

Primary citation

Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. McShan, A.C., Devlin, C.A., Overall, S.A. et al. Proc Natl Acad Sci U S A (2019) 116:25602-25613. DOI 10.1073/pnas.1915562116 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…
3E6F 2.41 Å, MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…

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