3VJ6: MHC class Ib molecule Qa-1b

Structure of the MHC class Ib molecule Qa-1b. Determined by X-ray diffraction at 1.9 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,451
Mol. weight: 45.4 kDa
Ligands: NI
Released: 14 Mar 2012

Explore 3VJ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VJ6 contains 12 α-helices and 28 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: 10 helices, 18 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	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
α-helix	223-225	3
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: 2 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
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, D-37 alpha chain	A	protein	277	Mus musculus	P06339 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Mus musculus	P01887 (AlphaFold model)
Qdm peptide	P	protein	9	Mus musculus	P01897 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VJ6_1 H-2 class I histocompatibility antigen, D-37 alpha chain (chains A)
SPHSLRYFTTAVSRPGLGEPRFIIVGYVDDTQFVRFDSDAENPRMEPRARWIEQEGPEYW
ERETWKARDMGRNFRVNLRTLLGYYNQSNDESHTLQWMYGCDVGPDGRLLRGYCQEAYDG
QDYISLNEDLRSWTANDIASQISKHKSEAVDEAHQQRAYLQGPCVEWLHRYLRLGNETLQ
RSDPPKAHVTHHPRSEDEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWAAVVVPLGKEQYYTCHVYHEGLPEPLTLRWEPP

Sequence of entity 2 (B), FASTA

>3VJ6_2 Beta-2-microglobulin (chains B)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>3VJ6_3 Qdm peptide (chains P)
AMAPRTLLL

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	4

Primary citation

A structural basis for antigen presentation by the MHC class Ib molecule, Qa-1b. Zeng, L., Sullivan, L.C., Vivian, J.P. et al. J Immunol (2012) 188:302-310. DOI 10.4049/jimmunol.1102379 · PubMed

Other PDB entries of the same protein (UniProt P06339 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UMO 2.6 Å, Murine CD94-NKG2A receptor in complex with Qa-1b presenting AMAPRTLLL

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