6U3N: LS2.8/3.15 - DQ2-P.fluor-alpha1a complex

LS2.8/3.15 - DQ2-P.fluor-alpha1a complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Pseudomonas fluorescens
Chains: 5
Atoms: 6,478
Mol. weight: 97.89 kDa
Ligands: NAG
Released: 18 Dec 2019

Explore 6U3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U3N contains 24 α-helices and 71 β-strands across 5 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	10
β-strand	19-26	8	10
β-strand	30-34	5	10
β-strand	41-43	3	10
α-helix	46-50	5
α-helix	56-76	21
α-helix	82-85	4
β-strand	88-93	6	11
β-strand	103-112	10	11
β-strand	118-123	6	12
β-strand	132-134	3	11
α-helix	137	1
β-strand	138-139	2	11
β-strand	145-153	9	11
β-strand	161-166	6	12
β-strand	174	1	12
β-strand	177-178	2	12

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	10
β-strand	23-31	9	10
β-strand	36-41	6	10
β-strand	47-49	3	10
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-71	7
α-helix	74	1
α-helix	75-80	6
α-helix	81-87	7
α-helix	90-92	3
β-strand	95	1	13
β-strand	98-102	5	14
β-strand	115-122	8	14
β-strand	123	1	13
β-strand	128-133	6	15
β-strand	136-137	2	15
β-strand	142-144	3	14
β-strand	148-149	2	14
β-strand	155-161	7	14
β-strand	172-176	5	15
α-helix	183	1
β-strand	184-186	3	15

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9

Chain D: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-14	5	2
β-strand	19-21	3	1
β-strand	24-25	2	1
β-strand	38-44	7	2
β-strand	51-56	6	2
β-strand	64-66	3	1
β-strand	77-81	5	1
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	100-108	9	2
β-strand	115-118	4	2
β-strand	122-127	6	2
β-strand	136-140	5	3
β-strand	141-142	2	4
β-strand	150-154	5	3
β-strand	171-173	3	3
α-helix	176	1
β-strand	177-178	2	4
α-helix	179	1
β-strand	189-193	5	3
α-helix	201-203	3
β-strand	214	1	3

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	5
β-strand	10-14	5	6
β-strand	19-24	6	5
α-helix	25-26	2
β-strand	38-44	7	6
β-strand	51-57	7	6
β-strand	65-68	4	6
β-strand	76-80	5	5
β-strand	87-91	5	5
α-helix	96-98	3
β-strand	100-107	8	6
β-strand	117-118	2	6
β-strand	122-127	6	6
β-strand	134	1	7
α-helix	135-136	2
β-strand	137-142	6	4
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	4
β-strand	164	1	7
β-strand	168-174	7	8
β-strand	177-179	3	8
β-strand	183-185	3	4
β-strand	190-191	2	4
β-strand	201-210	10	4
α-helix	211-214	4
β-strand	220-227	8	8
β-strand	230	1	9
α-helix	241-242	2
β-strand	244	1	9
β-strand	246-253	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-CELL RECEPTOR, LS2.8/3.15 alpha	D	protein	206	Homo sapiens
T-CELL RECEPTOR, LS2.8/3.15 beta	E	protein	244	Homo sapiens
MHC class II HLA-DQ-alpha chain	A	protein	191	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B	protein	206	Homo sapiens	O19712 (AlphaFold model)
Peptide	C	protein	20	Pseudomonas fluorescens

Sequence of entity 1 (D), FASTA

>6U3N_1 T-CELL RECEPTOR, LS2.8/3.15 alpha (chains D)
QSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQGIK
GFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVGAGSNYQLIWGAGTKLIIKPDIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (E), FASTA

>6U3N_2 T-CELL RECEPTOR, LS2.8/3.15 beta (chains E)
HMGVTQSPTHLIKTRGQQVTLRCSPISGHKSVSWYQQVLGQGPQFIFQYYEKEERGRGNF
PDRFSARQFPNYSSELNVNALLLGDSALYLCASSLEGQGASEQFFGPGTRLTVLEDLNKV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 3 (A), FASTA

>6U3N_3 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 4 (B), FASTA

>6U3N_4 MHC class II HLA-DQ-beta-1 (chains B)
GGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLG
LPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNL
LVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCH
VEHPSLQSPITVEWRAQSTGGDDDDK

Sequence of entity 5 (C), FASTA

>6U3N_5 Peptide (chains C)
APMPMPELPYPGSGGSIEGR

Ligands and cofactors

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

Primary citation

T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease. Petersen, J., Ciacchi, L., Tran, M.T. et al. Nat Struct Mol Biol (2020) 27:49-61. DOI 10.1038/s41594-019-0353-4 · 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

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