9QWJ: S2c TCR

Crystal structure of S2c TCR in complex with CD1c. Determined by X-ray diffraction at 2.04 Å resolution. Released 20 Aug 2025.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 6
Atoms: 13,571
Mol. weight: 203.2 kDa
Ligands: NAG, BMA, D12, CA
Released: 20 Aug 2025

Explore 9QWJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QWJ contains 63 α-helices and 149 β-strands across 6 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 B: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	5-6	2
β-strand	7-12	6	2
β-strand	22-31	10	2
β-strand	32	1	1
β-strand	37-42	6	3
β-strand	45-46	2	3
α-helix	47	1
β-strand	51-52	2	2
α-helix	53-55	3
β-strand	56-57	2	2
β-strand	63-71	9	2
β-strand	79-84	6	3
β-strand	92-95	4	3
β-strand	102	1	2
β-strand	117-130	14	4
β-strand	133-142	10	4
β-strand	145-151	7	4
β-strand	156-159	4	4
α-helix	170-195	26
α-helix	199-201	3
β-strand	204-215	12	4
β-strand	221-228	8	4
β-strand	231-237	7	4
β-strand	240-243	4	4
α-helix	245-247	3
α-helix	248-260	13
α-helix	263-271	9
α-helix	272-276	5
α-helix	277-287	11
α-helix	289-292	4
β-strand	296	1	5
α-helix	297-298	2
β-strand	299-306	8	6
β-strand	313-322	10	6
β-strand	323	1	5
β-strand	328-333	6	7
β-strand	336-337	2	7
α-helix	338	1
β-strand	341-343	3	6
β-strand	347-348	2	6
β-strand	354-361	8	6
β-strand	370-375	6	7
α-helix	377-379	3
β-strand	384-387	4	7

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
α-helix	10	1
β-strand	11-14	4	9
β-strand	19-21	3	10
β-strand	23-25	3	8
β-strand	32-38	7	9
β-strand	45-50	6	9
β-strand	56-59	4	10
β-strand	62-65	4	10
β-strand	67	1	8
α-helix	68-70	3
β-strand	72	1	8
β-strand	75-77	3	10
α-helix	82-84	3
β-strand	86-93	8	9
α-helix	95-97	3
α-helix	100	1
β-strand	101-103	3	9
β-strand	107-112	6	9
β-strand	121-126	6	11
β-strand	127	1	12
β-strand	134-139	6	11
α-helix	148-150	3
β-strand	155-157	3	11
α-helix	158-160	3
β-strand	161-165	5	11
α-helix	166-168	3
β-strand	170-179	10	11
α-helix	186-189	4

Chain E: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
α-helix	25-26	2
β-strand	31-37	7	14
β-strand	44-50	7	14
β-strand	53-57	5	14
β-strand	65-68	4	13
β-strand	75-79	5	13
α-helix	84-86	3
β-strand	88-95	8	14
α-helix	102-104	3
β-strand	105-106	2	14
β-strand	110-115	6	14
α-helix	118-120	3
β-strand	122	1	15
α-helix	123-124	2
β-strand	125-129	5	12
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	12
β-strand	152	1	15
β-strand	156-162	7	16
β-strand	165-167	3	16
β-strand	171-173	3	12
α-helix	177	1
β-strand	178-179	2	12
β-strand	189-198	10	12
α-helix	199-202	4
β-strand	208-215	8	16
β-strand	218	1	17
α-helix	229-230	2
β-strand	232	1	17
β-strand	234-241	8	16

Chain N: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	18
α-helix	5-6	2
β-strand	7-12	6	19
β-strand	22-31	10	19
β-strand	32	1	18
β-strand	37-42	6	20
β-strand	45-46	2	20
α-helix	47	1
β-strand	51-52	2	19
α-helix	53-55	3
β-strand	56-57	2	19
β-strand	63-71	9	19
β-strand	79-84	6	20
β-strand	92-95	4	20
β-strand	102	1	19
β-strand	119-130	12	21
β-strand	133-142	10	21
β-strand	145-151	7	21
β-strand	156-159	4	21
α-helix	170-195	26
α-helix	199-201	3
β-strand	204-213	10	21
β-strand	221-228	8	21
β-strand	231-237	7	21
β-strand	240-243	4	21
α-helix	249-260	12
α-helix	263-271	9
α-helix	272-276	5
α-helix	277-287	11
α-helix	289-292	4
β-strand	296	1	22
α-helix	297-298	2
β-strand	299-306	8	23
β-strand	313-322	10	23
β-strand	323	1	22
β-strand	328-332	5	24
β-strand	337	1	24
α-helix	338	1
β-strand	341-343	3	23
α-helix	344-346	3
β-strand	347-348	2	23
β-strand	354-361	8	23
β-strand	371-375	5	24
α-helix	377-379	3
β-strand	384-387	4	24

Chain T: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	25
β-strand	11-14	4	26
β-strand	19-21	3	27
β-strand	23-25	3	25
β-strand	32-38	7	26
β-strand	45-50	6	26
β-strand	56-59	4	27
β-strand	62-65	4	27
β-strand	67	1	25
α-helix	68-70	3
β-strand	72	1	25
β-strand	75-77	3	27
α-helix	82-84	3
β-strand	86-93	8	26
α-helix	95-97	3
β-strand	101-103	3	26
β-strand	107-112	6	26
β-strand	121-126	6	28
β-strand	134-139	6	28
α-helix	148-150	3
β-strand	155-157	3	28
α-helix	158-160	3
β-strand	161-165	5	28
α-helix	166-168	3
β-strand	170-179	10	28
α-helix	186-188	3

Chain U: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
β-strand	10-14	5	30
β-strand	19-24	6	29
α-helix	25	1
β-strand	31-37	7	30
β-strand	44-50	7	30
β-strand	53-57	5	30
β-strand	65-68	4	29
β-strand	75-79	5	29
α-helix	84-86	3
β-strand	88-95	8	30
α-helix	102-104	3
β-strand	105-106	2	30
β-strand	110-115	6	30
α-helix	118-120	3
β-strand	122	1	31
α-helix	123-124	2
β-strand	125-129	5	32
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	32
β-strand	152	1	31
β-strand	156-162	7	33
β-strand	165-167	3	33
β-strand	171-173	3	32
α-helix	177	1
β-strand	178-179	2	32
β-strand	189-198	10	32
α-helix	199-202	4
β-strand	208-215	8	33
β-strand	218	1	34
β-strand	232	1	34
β-strand	234-241	8	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin,T-cell surface glycoprotein CD1c	B, N	protein	442	Homo sapiens	P29017 (AlphaFold model), P61769 (AlphaFold model)
TCR alpha	D, T	protein	199	Homo sapiens
TCR beta	E, U	protein	246	Homo sapiens

Sequence of entity 1 (B, N), FASTA

>9QWJ_1 Beta-2-microglobulin,T-cell surface glycoprotein CD1c (chains B, N)
MYRMQLLSCIALSLALVTNSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLL
KNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDIG
GGGSGGGGSGGGGSEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLH
NWSKGNFSNEELSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPE
GFFQVAFNGLDLLSFQNTTWVPSPGCGSLAQSVCHLLNHQYEGVTETVYNLIRSTCPRFL
LGLLDAGKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWMRNEQEQLGT
KHGDILPNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGSLSTPPTPSTPP
TGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (D, T), FASTA

>9QWJ_2 TCR alpha (chains D, T)
MGNSVTQMEGPVTLSEEAFLTINCTYTATGYPSLFWYVQYPGEGLQLLLKATKADDKGSN
KGFEATYRKETTSFHLEKGSVQVSDSAVYFCALSDQYGWGKLQFGAGTQVVVTPDIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPED

Sequence of entity 3 (E, U), FASTA

>9QWJ_3 TCR beta (chains E, U)
MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSPRTGRGAEAFFGQGTRLTVVEDLN
KVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
BMA	beta-D-mannopyranose	C6 H12 O6	2
D12	Dodecane	C12 H26	2
CA	Calcium ion	Ca	3
D10	Decane	C10 H22	2

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

Primary citation

A CD1c lipid agnostic T cell receptor bispecific engager redirects T cells against CD1c + cells. Szoke-Kovacs, R., Khakoo, S., Rangel, V.L. et al. Front Immunol (2025) 16:1614610-1614610. DOI 10.3389/fimmu.2025.1614610 · PubMed

Other PDB entries of the same protein (UniProt P29017 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MX4 1.73 Å, CD1c with antigen analogue 1
7MXF 2.0 Å, CD1c with antigen analogue 2
7MXH 2.11 Å, CD1c with antigen analogue 3
9QWK 2.27 Å, Crystal structure of S2c-a5b6 TCR in complex with CD1c
5C9J 2.4 Å, Human CD1c with ligands in A' and F' channel
3OV6 2.5 Å, CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)
4ONO 2.71 Å, CD1c in complex with PM (phosphomycoketide)
6C09 2.95 Å, Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex
6C15 3.21 Å, CD1c in complex with phosphatidylcholine

Browse structure collections

About this viewer

MolViewer shows 9QWJ 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.