4OZF: JR5.1 protein complex

JR5.1 protein complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 5
Atoms: 6,624
Mol. weight: 97.5 kDa
Ligands: NAG
Released: 16 Apr 2014

Explore 4OZF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OZF contains 23 α-helices and 72 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, 15 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	81-83	3
β-strand	85	1	2
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	113	1	2
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-31	9	1
β-strand	36-41	6	1
β-strand	46-49	4	1
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	90-92	3
β-strand	95	1	5
β-strand	98-103	6	6
β-strand	114-122	9	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	136-138	3	7
β-strand	142-144	3	6
β-strand	148-149	2	6
β-strand	155-162	8	6
β-strand	170-176	7	7
β-strand	184-189	6	7

Chain G: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	38-44	7	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	66-67	2	8
β-strand	77-80	4	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-107	8	9
β-strand	122-127	6	9
β-strand	136-140	5	10
β-strand	141-142	2	11
β-strand	150-154	5	10
α-helix	162-165	4
β-strand	170-180	11	10
α-helix	181-183	3
β-strand	185-194	10	10
β-strand	215	1	10

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	38-44	7	13
β-strand	50-57	8	13
β-strand	64-67	4	13
β-strand	69	1	14
β-strand	71	1	14
β-strand	76-79	4	12
β-strand	87-91	5	12
α-helix	96-98	3
β-strand	100-107	8	13
α-helix	114-116	3
β-strand	117-118	2	13
β-strand	122-127	6	13
β-strand	134	1	15
β-strand	137-142	6	11
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	11
β-strand	164	1	15
β-strand	168-174	7	16
β-strand	177-179	3	16
β-strand	183-185	3	11
α-helix	189	1
β-strand	190-191	2	11
β-strand	201-210	10	11
α-helix	211-215	5
β-strand	220-227	8	16
β-strand	230	1	17
α-helix	241-242	2
β-strand	244	1	17
β-strand	246-253	8	16

Chain J: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	10-11	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	protein	191	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B	protein	213	Homo sapiens	P01920 (AlphaFold model)
T-cell receptor, JR5.1 alpha chain	G	protein	202	Homo sapiens	Q2YD82 (AlphaFold model)
T-cell receptor, JR5.1 beta chain	H	protein	244	Homo sapiens	P01850 (AlphaFold model)
deamidated Gliadin-alpha2 peptide	J	protein	13	Triticum aestivum	P04722

Sequence of entity 1 (A), FASTA

>4OZF_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B), FASTA

>4OZF_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B)
GGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEF
RAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTE
ALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQR
GDVYTCHVEHPSLQSPITVEWRAQSTGGDDDDK

Sequence of entity 3 (G), FASTA

>4OZF_3 T-CELL RECEPTOR, JR5.1 ALPHA CHAIN (chains G)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIAFQGAQKLVFGQGTRLTINPNIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (H), FASTA

>4OZF_4 T-CELL RECEPTOR, JR5.1 BETA CHAIN (chains H)
MGVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQGLEFLIYFQGNSAPDKSGLP
SDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSFRALAADTQYFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 5 (J), FASTA

>4OZF_5 deamidated Gliadin-alpha2 peptide (chains J)
APQPELPYPQPGS

Ligands and cofactors

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

Primary citation

T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease. Petersen, J., Montserrat, V., Mujico, J.R. et al. Nat Struct Mol Biol (2014) 21:480-488. DOI 10.1038/nsmb.2817 · 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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