6MFG: HLA-DQ2-glia-alpha1

HLA-DQ2-glia-alpha1. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,518
Mol. weight: 94.65 kDa
Ligands: NAG
Released: 21 Nov 2018

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

Secondary structure: helices and β-sheets

6MFG contains 27 α-helices and 56 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	11	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	46-50	5
α-helix	56-76	21
α-helix	81-85	5
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-127	2	9
β-strand	132-134	3	8
α-helix	137	1
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-178	5	9

Chain C: 4 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	81-85	5
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
α-helix	137	1
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 E: 10 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	117-124	8
α-helix	126-128	3
β-strand	131	1	4
α-helix	132-133	2
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	206-212	7	6
β-strand	220-225	6	6

Chain F: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1-9	9
β-strand	44-54	11	7
β-strand	59-68	10	7
β-strand	71-77	7	7
β-strand	83-85	3	7
α-helix	88-90	3
α-helix	91-99	9
α-helix	101-110	10
α-helix	111-116	6
α-helix	117-124	8
α-helix	126-128	3
β-strand	131	1	10
α-helix	132-133	2
β-strand	134-139	6	11
β-strand	150-158	9	11
β-strand	159	1	10
β-strand	164-169	6	12
β-strand	172-174	3	12
β-strand	178-180	3	11
α-helix	181-183	3
β-strand	184-185	2	11
β-strand	191-198	8	11
β-strand	207-212	6	12
β-strand	220-224	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	protein	190	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein	E, F	protein	226	Homo sapiens	O19712 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6MFG_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPESGDDDDK

Sequence of entity 2 (E, F), FASTA

>6MFG_2 MHC class II HLA-DQ-beta-1 - DQ2-glia-alpha1 chimeric protein (chains E, F)
QPFPQPELPYPGSGGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNR
EEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRR
VEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWT
FQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSTGGDDDDK

Ligands and cofactors

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

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
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
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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