2ZSV: H-2Kb

Crystal structure of H-2Kb in complex with JHMV epitope S598. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Nov 2008.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,920
Mol. weight: 90.48 kDa
Ligands: CYS
Released: 4 Nov 2008

Explore 2ZSV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZSV contains 23 α-helices and 60 β-strands across 6 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: 8 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	165-175	11
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

Chains B and D: 2 helices, 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
α-helix	52-54	3
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: 9 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	50-54	5
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	140-149	10
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-179	15
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	222-223	2	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	270-272	3	11

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, K-B alpha chain	A, C	protein	278	Mus musculus	P01901 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Mus musculus	P01887 (AlphaFold model)
8-mer peptide from spike glycoprotein	E, F	protein	8		P11225

Sequence of entity 1 (A, C), FASTA

>2ZSV_1 H-2 class I histocompatibility antigen, K-B alpha chain (chains A, C)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPP

Sequence of entity 2 (B, D), FASTA

>2ZSV_2 Beta-2-microglobulin (chains B, D)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (E, F), FASTA

>2ZSV_3 8-mer peptide from spike glycoprotein (chains E, F)
RAQIFANI

Ligands and cofactors

ID	Name	Formula	Copies
CYS	Cysteine	C3 H7 N O2 S	1

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

Primary citation

Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant. Butler, N.S., Theodossis, A., Webb, A.I. et al. PLoS Pathog (2008) 4. DOI 10.1371/journal.ppat.1000186 · 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…
1FZK 1.7 Å, MHC class I natural mutant H-2KBM1 heavy chain complexed with beta-2 microglobulin and…
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

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