5OQG: PDB entry 5OQG

Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb W167A, beta-2microglobulin, and and ovalbumin-derived peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 11 Apr 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,184
Mol. weight: 96.13 kDa
Released: 11 Apr 2018

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

Secondary structure: helices and β-sheets

5OQG contains 25 α-helices and 60 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: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	26	1	1
α-helix	27-28	2
β-strand	29-34	6	2
β-strand	44-53	10	2
β-strand	54	1	1
β-strand	59-64	6	3
β-strand	67-68	2	3
β-strand	73-74	2	2
α-helix	75-77	3
β-strand	78-79	2	2
β-strand	85-93	9	2
β-strand	101-106	6	3
β-strand	114-117	4	3
β-strand	145-154	10	4
α-helix	162	1
β-strand	163-170	8	4
β-strand	173-179	7	4
β-strand	188-189	2	4
α-helix	192-194	3
α-helix	199-226	28
β-strand	236-245	10	4
β-strand	251-260	10	4
β-strand	263-268	6	4
β-strand	275-277	3	4
α-helix	282-292	11
α-helix	294-301	8
α-helix	302-306	5
α-helix	307-316	10
β-strand	325	1	5
α-helix	326-327	2
β-strand	328-335	8	6
β-strand	340-350	11	6
β-strand	351	1	5
β-strand	356-361	6	7
β-strand	364-365	2	7
β-strand	371-372	2	6
β-strand	376-377	2	6
β-strand	383-392	10	6
α-helix	396-398	3
β-strand	399-404	6	7
β-strand	412-414	3	7

Chain B: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	26	1	8
α-helix	27-28	2
β-strand	29-34	6	9
β-strand	44-53	10	9
β-strand	54	1	8
β-strand	59-64	6	10
β-strand	67-68	2	10
β-strand	73-74	2	9
α-helix	75-77	3
β-strand	78-79	2	9
β-strand	85-93	9	9
β-strand	101-106	6	10
β-strand	114-117	4	10
β-strand	145-154	10	11
α-helix	162	1
β-strand	163-170	8	11
β-strand	173-179	7	11
β-strand	188-189	2	11
α-helix	192-196	5
α-helix	199-226	28
β-strand	236-245	10	11
β-strand	251-260	10	11
β-strand	263-268	6	11
β-strand	275-277	3	11
α-helix	280-292	13
α-helix	294-300	7
α-helix	301-306	6
α-helix	307-321	15
β-strand	325	1	12
α-helix	326-327	2
β-strand	328-335	8	13
β-strand	340-350	11	13
β-strand	351	1	12
β-strand	356-361	6	14
β-strand	364-365	2	14
β-strand	371-372	2	13
α-helix	373-375	3
β-strand	376-377	2	13
β-strand	383-392	10	13
α-helix	396-398	3
β-strand	399-404	6	14
β-strand	412-414	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain	A, B	protein	431	Mus musculus	P01887 (AlphaFold model), P01901 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5OQG_1 Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain (chains A, B)
SIINFEKLGCGASGGGGSGGGGSIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEI
QMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDR
DMGGGGSGGGGSGGGGSGGGGSGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDS
DAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRTLLGCYNQSKGGSHTIQVI
SGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRA
YLEGTCVEALRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQ
LNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPP
STVSNHHHHHH

Primary citation

The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1. Papakyriakou, A., Reeves, E., Beton, M. et al. J Biol Chem (2018) 293:7538-7548. DOI 10.1074/jbc.RA117.000313 · PubMed

Other PDB entries of the same protein (UniProt P01887 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3G08 1.6 Å, Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d
3GMO 1.6 Å, Structure of mouse CD1d in complex with C8PhF
7LFK 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant, refined…
7LFL 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
7LFM 1.6 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant,…
6C6F 1.67 Å, Structure of glycolipid aGSA[26,P5p] in complex with mouse CD1d
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…

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