7RYO: CD1a-dideoxymycobactin-gdTCR complex

CD1a-dideoxymycobactin-gdTCR complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 18 May 2022.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,288
Mol. weight: 97.86 kDa
Ligands: WGR
Released: 18 May 2022

Explore 7RYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RYO contains 20 α-helices and 73 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	24-31	8	1
β-strand	36-41	6	1
β-strand	46-49	4	1
α-helix	52-55	4
α-helix	60-87	28
β-strand	94-104	11	1
β-strand	113-118	6	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	134	1
α-helix	135-137	3
α-helix	139-150	12
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
β-strand	236-237	2	3
β-strand	243-252	10	3
α-helix	253-255	3
β-strand	259-264	6	4
α-helix	266-268	3
β-strand	273-276	4	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	38-42	5	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-83	5	7
β-strand	92-95	4	7

Chain C: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	8
β-strand	20-25	6	9
β-strand	34-40	7	8
β-strand	47-53	7	8
β-strand	58-61	4	8
β-strand	70-73	4	9
β-strand	80-85	6	9
α-helix	89-91	3
β-strand	93-100	8	8
β-strand	107-109	3	8
β-strand	111	1	10
β-strand	113-118	6	8
α-helix	121-123	3
β-strand	125	1	11
β-strand	128-132	5	12
α-helix	133-135	3
α-helix	136-139	4
β-strand	144-146	3	13
β-strand	148-154	7	12
β-strand	155	1	11
β-strand	159-165	7	14
β-strand	168-170	3	14
β-strand	174-176	3	12
β-strand	181-182	2	12
β-strand	192-198	7	12
β-strand	199-201	3	13
α-helix	202-205	4
β-strand	211-218	8	14
β-strand	221	1	15
α-helix	232-233	2
β-strand	235	1	15
β-strand	237-244	8	14

Chain D: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	11-15	5	10
β-strand	20-27	8	16
β-strand	33-41	9	10
β-strand	45-53	9	10
α-helix	57-59	3
β-strand	60-61	2	16
β-strand	64-69	6	16
β-strand	74-79	6	16
β-strand	88-96	9	10
β-strand	104-105	2	10
β-strand	109-114	6	10
β-strand	123-128	6	17
β-strand	129	1	12
β-strand	136-141	6	17
β-strand	158-159	2	17
β-strand	164	1	12
β-strand	176-180	5	17
α-helix	188-191	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1a	A	protein	286	Homo sapiens	P06126 (AlphaFold model)
Beta-2-microglobulin	B	protein	108	Homo sapiens	P61769 (AlphaFold model)
T cell receptor gamma variable 4,T cell receptor beta constant 1	C	protein	248	Homo sapiens	A0A0C4DH28 (AlphaFold model), P01850 (AlphaFold model)
T cell receptor delta variable 1,T cell receptor alpha chain constant	D	protein	209	Homo sapiens	A0A1B0GX56, P01848

Sequence of entity 1 (A), FASTA

>7RYO_1 T-cell surface glycoprotein CD1a (chains A)
DAATGLKEPLSFHVIWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLWPWSRGNF
SNEEWKELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAY
QGSDFVSFQNNSWLPYPVAGNMAKHFCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGK
AHLQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQRGDILPS
ADGTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEGSLVPR

Sequence of entity 2 (B), FASTA

>7RYO_2 Beta-2-microglobulin (chains B)
DAGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGSLVPR

Sequence of entity 3 (C), FASTA

>7RYO_3 T cell receptor gamma variable 4,T cell receptor beta constant 1 (chains C)
MASSNLEGRTKSVIRQTGSSAEITCDLAEGSTGYIHWYLHQEGKAPQRLLYYDSYTSSVV
LESGISPGKYDTYGSTRKNLRMILRNLIENDSGVYYCATWDGDYYKKLFGSGTTLVVTED
LKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQP
LKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVS
AEAWGRAD

Sequence of entity 4 (D), FASTA

>7RYO_4 T cell receptor delta variable 1,T cell receptor alpha chain constant (chains D)
MAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAK
SGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGELRWPDKLIFGKGTRVTVEPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Ligands and cofactors

ID	Name	Formula	Copies
WGR	dideoxymycobactin-838	C47 H75 N5 O8	1

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors. Wegrecki, M., Ocampo, T.A., Gunasinghe, S.D. et al. Nat Commun (2022) 13:3872-3872. DOI 10.1038/s41467-022-31443-9 · PubMed

Other PDB entries of the same protein (UniProt P06126 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J1A 1.86 Å, Antigen presenting molecule
4X6F 1.91 Å, CD1a binary complex with sphingomyelin
7SH4 2.0 Å, CD1a-phosphatidylglycerol binary structure
7KP1 2.02 Å, CD1a-42:2 SM binary complex
4X6E 2.1 Å, CD1a binary complex with lysophosphatidylcholine
9OHZ 2.14 Å, Crystal structure of CD1a presenting ganglioside GD3
1ONQ 2.15 Å, Crystal Structure of CD1a in Complex with a Sulfatide
6NUX 2.2 Å, CD1a-lipid binary complex
7KOZ 2.25 Å, CD1a-36:2 SM binary complex
7KP0 2.4 Å, CD1a-42:1 SM binary complex
7RYN 2.7 Å, CD1a-sulfatide-gdTCR complex
1XZ0 2.8 Å, Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide

Browse structure collections

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