6CUG: BC8B TCR-CD1b-PC complex

Crystal structure of BC8B TCR-CD1b-PC complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,820
Mol. weight: 97.24 kDa
Ligands: POV, CUY, NAG
Released: 16 Jan 2019

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

Secondary structure: helices and β-sheets

6CUG contains 23 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-88	29
α-helix	90-91	2
β-strand	94-104	11	1
α-helix	105	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	135-137	3
α-helix	139-148	10
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
α-helix	194-196	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	216-222	7	4
β-strand	225-226	2	4
β-strand	230-232	3	3
β-strand	236-238	3	3
β-strand	242-252	11	3
β-strand	260-265	6	4
β-strand	273-276	4	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
α-helix	6-7	2
β-strand	8-13	6	6
β-strand	23-32	10	6
β-strand	33	1	5
β-strand	38-43	6	7
β-strand	46-47	2	7
β-strand	52-53	2	6
α-helix	54-56	3
β-strand	57-58	2	6
β-strand	64-72	9	6
β-strand	80-85	6	7
β-strand	93-96	4	7

Chain D: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	11-14	4	9
β-strand	19-21	3	10
β-strand	23-26	4	8
β-strand	31-38	8	9
β-strand	44-50	7	9
β-strand	56-59	4	10
β-strand	62-65	4	10
β-strand	67	1	8
β-strand	72	1	8
β-strand	75-77	3	10
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	102-103	2	9
β-strand	107-112	6	9
β-strand	121-127	7	11
β-strand	134-139	6	11
α-helix	145-149	5
β-strand	155-157	3	11
α-helix	158-160	3
β-strand	161-165	5	11
β-strand	170-179	10	11

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	31-38	8	13
β-strand	42-51	10	13
β-strand	54-57	4	13
β-strand	64-67	4	12
β-strand	73-78	6	12
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	105-106	2	13
β-strand	110-115	6	13
α-helix	118-120	3
β-strand	122	1	14
α-helix	123-124	2
β-strand	125-130	6	11
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	11
β-strand	152	1	14
β-strand	156-162	7	15
β-strand	165-167	3	15
β-strand	171-173	3	11
α-helix	177	1
β-strand	178-179	2	11
β-strand	189-198	10	11
α-helix	199-203	5
β-strand	208-215	8	15
β-strand	218	1	16
α-helix	229-230	2
β-strand	232	1	16
β-strand	234-241	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1b	A	protein	300	Homo sapiens	P29016 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor alpha variable TRAV9-2 - BC8B TCR	D	protein	207	Homo sapiens
T-cell receptor beta variable TRBV6-2 - BC8B TCR	E	protein	245	Homo sapiens

Sequence of entity 1 (A), FASTA

>6CUG_1 T-cell surface glycoprotein CD1b (chains A)
HAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDK
EVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGL
DFLSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKADL
QRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANW
TWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B), FASTA

>6CUG_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>6CUG_3 T-cell receptor alpha variable TRAV9-2 - BC8B TCR (chains D)
GNSVTQMEGPVTLSEEAFLTINCTYTATGYPSLFWYVQYPGEGLQLLLKATKADDKGSNK
GFEATYRKETTSFHLEKGSVQVSDSAVYFCALTPSGGYQKVTFGTGTKLQVIPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>6CUG_4 T-cell receptor beta variable TRBV6-2 - BC8B TCR (chains E)
NAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEV
PDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSMPGLRSSYEQYFGPGTRLTVTEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	1
CUY	tetracosyl octadecanoate	C42 H84 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids. Shahine, A., Reinink, P., Reijneveld, J.F. et al. Nat Commun (2019) 10:56-56. DOI 10.1038/s41467-018-07898-0 · PubMed

Other PDB entries of the same protein (UniProt P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
9OI0 1.84 Å, Crystal structure of CD1b presenting ganglioside GD3
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
3T8X 1.9 Å, Crystal structure of human CD1b in complex with synthetic antigenic…
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1

Browse structure collections

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