1FZK: MHC class I natural mutant H-2KBM1 heavy chain

MHC class I natural mutant H-2KBM1 heavy chain complexed with beta-2 microglobulin and sendai virus nucleoprotein. Determined by X-ray diffraction at 1.7 Å resolution. Released 28 Mar 2001.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,677
Mol. weight: 45.65 kDa
Ligands: MRD, PO4, NAG
Released: 28 Mar 2001

Explore 1FZK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1FZK contains 12 α-helices and 29 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: 9 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	57-84	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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-194	9	3
β-strand	198-208	11	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	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 10 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
α-helix	46	1
α-helix	49	1
β-strand	50-56	7	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, K-B alpha chain	A	protein	274	Mus musculus	P01901 (AlphaFold model)
Protein (beta-2-microglobulin)	B	protein	99	Mus musculus	P01887 (AlphaFold model)
Protein (nucleocapsid protein)	P	protein	9		P04857

Sequence of entity 1 (A), FASTA

>1FZK_1 H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN (chains A)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGAAEYYRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>1FZK_2 PROTEIN (BETA-2-MICROGLOBULIN) (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>1FZK_3 PROTEIN (NUCLEOCAPSID PROTEIN) (chains P)
FAPGNYPAL

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	1
PO4	Phosphate ion	O4 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. Rudolph, M.G., Speir, J.A., Brunmark, A. et al. Immunity (2001) 14:231-242. DOI 10.1016/S1074-7613(01)00105-4 · PubMed

Other PDB entries of the same protein (UniProt P01901 (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
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3TID 1.65 Å, Crystal structure of the LCMV derived peptide GP34 in complex with the murine mhc class…
1KPV 1.71 Å, High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
1LEG 1.75 Å, Crystal Structure of H-2Kb bound to the dEV8 peptide
6GB6 1.78 Å, Structure of H-2Kb with dipeptide GL
1FZM 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1FZO 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1T0N 1.8 Å, Conformational switch in polymorphic H-2K molecules containing an HSV peptide
2QRT 1.8 Å, Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy…

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