7LFK: Histocompatibility 2, M region locus 3

Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant, refined at 1.60 Å resolution. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,735
Mol. weight: 90.9 kDa
Ligands: NAG
Released: 14 Jul 2021

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

Secondary structure: helices and β-sheets

7LFK contains 26 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	15-16	2
β-strand	22-28	7	1
β-strand	31-39	9	1
β-strand	42-47	6	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	153-159	7
α-helix	160-164	5
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	1	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: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
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	78-84	7	7
β-strand	91-94	4	7

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	15-16	2
β-strand	22-28	7	8
β-strand	31-39	9	8
β-strand	42-47	6	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	138-150	13
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-174	10
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	214-219	6	11
β-strand	222-223	2	11
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	257-262	6	11
β-strand	270-272	3	11

Chain E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
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
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histocompatibility 2, M region locus 3	A, D	protein	282	Mus musculus	Q31093 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Heptapeptide from NADH-ubiquinone oxidoreductase chain 1	C, F	protein	7	Mus musculus	P03888 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7LFK_1 Histocompatibility 2, M region locus 3 (chains A, D)
GSHSLRYFHTAVSRPGRGEPQYISVGYVDDVQFQRCDSIEEIPRMEPRAPWMEKERPEYW
KELKLKVKNIAQSARANLRTLLRYYNQSEGGSHILQWMVSCEVGPDMRLLGAHYQAAYDG
SDYITLNEDLSSWTAVDMVSQITKSRLESAGTAEYFRAYVEGECLELLHRFLRNGKEILQ
RADPPKAHVAHHPRPKGDVTLRCWALGFYPADITLTWQKDEEDLTQDMELVETRPSGDGT
FQKWAAVVVPSGEEQRYTCYVHHEGLTEPLALKWRSHHHHHH

Sequence of entity 2 (B, E), FASTA

>7LFK_2 Beta-2-microglobulin (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>7LFK_3 Heptapeptide from NADH-ubiquinone oxidoreductase chain 1 (chains C, F)
MFFINTL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides. Strand, A., Shen, S.T., Tomchick, D.R. et al. J Biomol Struct Dyn (2022) 40:10300-10312. DOI 10.1080/07391102.2021.1942214 · PubMed

Other PDB entries of the same protein (UniProt Q31093 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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,…
7LFI 1.7 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide refined at 1.70 Å…
7LFJ 1.7 Å, Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, ala mutant, refined…
1MHC 2.1 Å, Model of MHC class I H2-M3 with nonapeptide from rat ND1 refined at 2.3 Å resolution

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