5KD7: Murine MHC-I H-2Dd

Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV). Determined by X-ray diffraction at 2.35 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Mus musculus, Human immunodeficiency virus type 1 group M subtype B (isolate MN)
Chains: 12
Atoms: 12,650
Mol. weight: 179.73 kDa
Released: 11 Oct 2017

Explore 5KD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KD7 contains 47 α-helices and 119 β-strands across 8 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	50-54	5
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	138-149	12
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
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
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	257-262	6	4
β-strand	270-272	3	4

Chain B: 1 helix, 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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 10 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	50-52	3
α-helix	57-85	29
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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222	1	11
β-strand	229-230	2	10
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-273	4	11

Chain D: 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
α-helix	14-15	2
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	35-41	7	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	78-84	7	14
β-strand	91-94	4	14

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	52-54	3
α-helix	57-85	29
β-strand	94-104	11	15
β-strand	108-118	11	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-218	5	18
β-strand	223	1	18
β-strand	229-230	2	17
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	258-262	5	18
β-strand	270-272	3	18

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	21-30	10	20
β-strand	31	1	19
β-strand	36-41	6	21
β-strand	44-45	2	21
β-strand	50	1	20
β-strand	55-56	2	20
β-strand	62-70	9	20
β-strand	78-83	6	21
β-strand	91-94	4	21

Chain I: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	22
α-helix	20	1
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	45-47	3	22
α-helix	50-54	5
α-helix	57-85	29
β-strand	94-103	10	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
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	23
α-helix	184-185	2
β-strand	186-193	8	24
β-strand	199-208	10	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222-223	2	25
β-strand	230	1	24
β-strand	234-235	2	24
β-strand	241-249	9	24
β-strand	257-262	6	25
β-strand	271-272	2	25

Chain J: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	26
α-helix	4-5	2
β-strand	6-11	6	27
β-strand	21-30	10	27
β-strand	31	1	26
β-strand	36-41	6	28
β-strand	44-45	2	28
α-helix	46	1
β-strand	50-51	2	27
α-helix	52-54	3
β-strand	55-56	2	27
β-strand	62-70	9	27
β-strand	78-83	6	28
β-strand	91-94	4	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, C, F, I	protein	275	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, D, G, J	protein	100	Mus musculus	P01887 (AlphaFold model)
Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV)	E, H, K, P	protein	9	Human immunodeficiency virus type 1 group M subtype B (isolate MN)	P05877

Sequence of entity 1 (A, C, F, I), FASTA

>5KD7_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, C, F, I)
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC
DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGK

Sequence of entity 2 (B, D, G, J), FASTA

>5KD7_2 Beta-2-microglobulin (chains B, D, G, J)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (E, H, K, P), FASTA

>5KD7_3 Peptide (PV9) of HIV gp120 MN isolate (IGPGRAFYV) (chains E, H, K, P)
IGPGRAFYV

Primary citation

Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity. Frey, B.F., Jiang, J., Sui, Y. et al. J Immunol (2018) 200:1853-1864. DOI 10.4049/jimmunol.1701523 · 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
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
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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