6MFF: HLA-DQ2-glia-omega1

HLA-DQ2-glia-omega1. Determined by X-ray diffraction at 2.6 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,052
Mol. weight: 47.66 kDa
Ligands: NAG
Released: 21 Nov 2018

Explore 6MFF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MFF 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-50	5
α-helix	56-76	21
α-helix	82-84	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-128	3	3
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain C: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-9	9
β-strand	44-54	11	1
β-strand	59-68	10	1
β-strand	71-77	7	1
β-strand	83-85	3	1
α-helix	88-90	3
α-helix	91-99	9
α-helix	101-108	8
α-helix	110	1
α-helix	111-116	6
α-helix	117-123	7
α-helix	126-128	3
β-strand	131	1	4
β-strand	134-139	6	5
β-strand	150-158	9	5
β-strand	159	1	4
β-strand	164-169	6	6
β-strand	172-174	3	6
β-strand	178-180	3	5
α-helix	181-183	3
β-strand	184-185	2	5
β-strand	191-198	8	5
β-strand	207-212	6	6
β-strand	220-224	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	protein	190	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein	C	protein	226	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MFF_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPESGDDDDK

Sequence of entity 2 (C), FASTA

>6MFF_2 MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein (chains C)
QPFPQPEQPFPGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNR
EEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRR
VEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWT
FQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSTGGDDDDK

Ligands and cofactors

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

Primary citation

Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes. Dahal-Koirala, S., Ciacchi, L., Petersen, J. et al. J Biol Chem (2019) 294:941-952. DOI 10.1074/jbc.RA118.005736 · PubMed

Other PDB entries of the same protein (UniProt P01909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6U3M 1.9 Å, DQ2-P.fluor-alpha1a
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
6MFG 2.0 Å, HLA-DQ2-glia-alpha1
2NNA 2.1 Å, Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
8W84 2.1 Å, HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
5KSV 2.19 Å, Crystal structure of HLA-DQ2.5-CLIP2
9EJG 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
1S9V 2.22 Å, Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
8W86 2.24 Å, HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
1JK8 2.4 Å, Crystal structure of a human insulin peptide-HLA-DQ8 complex
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2

Browse structure collections

About this viewer

MolViewer shows 6MFF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.