4OZI: S2 protein complex

S2 protein complex. Determined by X-ray diffraction at 3.2 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Triticum aestivum
Chains: 10
Atoms: 12,849
Mol. weight: 195.92 kDa
Ligands: NAG, CA
Released: 16 Apr 2014

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

Secondary structure: helices and β-sheets

4OZI contains 45 α-helices and 140 β-strands across 10 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	57-76	20
α-helix	81-83	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
α-helix	135-137	3
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 B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	36-41	6	1
β-strand	47-49	3	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	4
β-strand	98-102	5	5
β-strand	114-120	7	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	137	1	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
β-strand	170-176	7	6
β-strand	186-189	4	6

Chain C: 4 helices, 15 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	57-76	20
α-helix	81-84	4
β-strand	85	1	8
α-helix	86-87	2
β-strand	88-93	6	9
β-strand	103-112	10	9
β-strand	113	1	8
β-strand	118-123	6	10
β-strand	126-127	2	10
β-strand	132-134	3	9
β-strand	138-139	2	9
β-strand	145-153	9	9
β-strand	161-166	6	10
β-strand	174-178	5	10

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	7
β-strand	23-31	9	7
β-strand	36-41	6	7
β-strand	47-49	3	7
α-helix	54-63	10
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	11
β-strand	98-103	6	12
β-strand	114-122	9	12
β-strand	123	1	11
β-strand	128-133	6	13
β-strand	136-137	2	13
β-strand	142-144	3	12
β-strand	148-149	2	12
β-strand	155-162	8	12
β-strand	171-176	6	13
β-strand	184-188	5	13

Chain E: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
β-strand	10-14	5	15
β-strand	19-24	6	14
β-strand	38-44	7	15
α-helix	49-50	2
β-strand	51-56	6	15
β-strand	66-67	2	14
β-strand	77-79	3	14
β-strand	86-91	6	14
α-helix	96-98	3
β-strand	101-107	7	15
β-strand	122-127	6	15
β-strand	136-140	5	16
β-strand	141	1	17
α-helix	142	1
β-strand	149-154	6	16
α-helix	162-165	4
β-strand	171-172	2	16
α-helix	173-175	3
β-strand	176-180	5	16
β-strand	185-194	10	16
β-strand	215	1	16

Chain F: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-14	5	19
β-strand	19-25	7	18
β-strand	38-44	7	19
β-strand	51-57	7	19
β-strand	59	1	20
β-strand	66-67	2	19
β-strand	76-79	4	18
β-strand	80	1	20
β-strand	86-91	6	18
α-helix	96-98	3
β-strand	101-106	6	19
β-strand	115-116	2	19
β-strand	120-125	6	19
α-helix	128-130	3
β-strand	132	1	21
β-strand	135-139	5	22
β-strand	140	1	17
α-helix	141-142	2
α-helix	143-148	6
β-strand	151-161	11	22
β-strand	162	1	21
β-strand	166-172	7	23
β-strand	175-177	3	23
β-strand	181-183	3	22
α-helix	187	1
β-strand	188-189	2	22
α-helix	197-198	2
β-strand	199-208	10	22
α-helix	209-213	5
β-strand	218-225	8	23
β-strand	228	1	24
α-helix	239-240	2
β-strand	242	1	24
β-strand	245-251	7	23

Chain G: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	25
β-strand	10-14	5	26
β-strand	19-24	6	25
β-strand	38-44	7	26
α-helix	45	1
α-helix	49-50	2
β-strand	51-56	6	26
β-strand	66-67	2	25
β-strand	77-79	3	25
β-strand	86-91	6	25
α-helix	96-98	3
β-strand	101-107	7	26
β-strand	122-127	6	26
β-strand	136-142	7	27
β-strand	149-154	6	27
β-strand	170-172	3	27
α-helix	173-175	3
β-strand	176-180	5	27
β-strand	185-194	10	27
α-helix	201-204	4
β-strand	215	1	27

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-25	7	28
β-strand	39-44	6	29
β-strand	51-56	6	29
β-strand	66-67	2	29
β-strand	76-79	4	28
β-strand	86-91	6	28
α-helix	96-98	3
β-strand	101-106	6	29
β-strand	115-116	2	29
β-strand	120-125	6	29
α-helix	128-130	3
β-strand	132	1	30
β-strand	135-140	6	27
α-helix	141-142	2
α-helix	143-148	6
β-strand	151-161	11	27
β-strand	162	1	30
β-strand	166-172	7	31
β-strand	175-177	3	31
β-strand	181-183	3	27
α-helix	187	1
β-strand	188-189	2	27
α-helix	197-198	2
β-strand	199-208	10	27
α-helix	209-212	4
β-strand	218-225	8	31
α-helix	239-240	2
β-strand	245-251	7	31

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, C	protein	191	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B, D	protein	213	Homo sapiens	P01920 (AlphaFold model)
T-cell receptor, s2, alpha chain	E, G	protein	207	Homo sapiens	Q2YD82 (AlphaFold model)
T-cell receptor, s2, beta chain	F, H	protein	244	Homo sapiens	P01850 (AlphaFold model)
deamidated Gliadin-alpha1 peptide	I, J	protein	13	Triticum aestivum	P04722

Sequence of entity 1 (A, C), FASTA

>4OZI_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, C)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPETSGDDDDK

Sequence of entity 2 (B, D), FASTA

>4OZI_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, D)
GGSIEGRGGSGASRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEF
RAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTE
ALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQR
GDVYTCHVEHPSLQSPITVEWRAQSTGGDDDDK

Sequence of entity 3 (E, G), FASTA

>4OZI_3 T-cell receptor, s2, alpha chain (chains E, G)
KTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVASL
FIPADRKSSTLSLPRVSLSDTAVYYCLVGDGGSFSGGYNKLIFGAGTRLAVHPYIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (F, H), FASTA

>4OZI_4 T-cell receptor, s2, beta chain (chains F, H)
MVVSQHPSWVICKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQG
VEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSAGVGGQETQYFGPGTRLLVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 5 (I, J), FASTA

>4OZI_5 deamidated Gliadin-alpha1 peptide (chains I, J)
QPFPQPELPYPGS

Ligands and cofactors

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

Browse structure collections

About this viewer

MolViewer shows 4OZI 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.