6V7Y: Human CD1d presenting alpha-Galactosylceramide

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Lama glama
Chains: 3
Atoms: 4,324
Mol. weight: 68.11 kDa
Ligands: NAG, AGH
Released: 16 Sept 2020

Explore 6V7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V7Y contains 17 α-helices and 42 β-strands across 3 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
α-helix	2-4	3
β-strand	7-15	9	1
β-strand	22-29	8	1
β-strand	32-37	6	1
β-strand	45-46	2	1
α-helix	57-85	29
α-helix	88	1
α-helix	90	1
β-strand	91-102	12	1
β-strand	106-115	10	1
β-strand	118-124	7	1
β-strand	127-130	4	1
α-helix	136-145	10
α-helix	149-157	9
α-helix	158-162	5
α-helix	163-173	11
α-helix	175-178	4
β-strand	182	1	2
β-strand	185-191	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-218	5	4
β-strand	224	1	4
β-strand	228-229	2	3
β-strand	233-234	2	3
β-strand	240-249	10	3
β-strand	257-261	5	4
α-helix	263-265	3
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain F: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	11-13	3	9
β-strand	18-24	7	8
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	46-51	6	10
α-helix	57-58	2
β-strand	59-60	2	10
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	10
α-helix	106-108	3
α-helix	111-113	3
β-strand	116-117	2	10
β-strand	121-123	3	10
β-strand	124-126	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	347	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Nanobody VHH ID5	F	protein	127	Lama glama

Sequence of entity 1 (A), FASTA

>6V7Y_1 Antigen-presenting glycoprotein CD1d (chains A)
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQW
ETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDI
LSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKK
QVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETW
YLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQN
SELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B), FASTA

>6V7Y_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (F), FASTA

>6V7Y_3 Nanobody VHH ID5 (chains F)
EVQLVESGGGLVQAGGSLRLSCAASGSSFSSYTMGWFRQAPGKEREIVAGIRWSDESPIY
ADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAARLVPPGIPIPRTSESMRYWGKG
TLVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	1

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

Primary citation

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response. Shahine, A., Rossjohn, J. Nat Cancer (2020). DOI 10.1038/s43018-020-00111-6

Other PDB entries of the same protein (UniProt P15813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RSE 1.76 Å, Human CD1d with lipid antigen bound
8SOS 2.33 Å, Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17
4WW2 2.48 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8,…
3HUJ 2.5 Å, Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant…
4WO4 2.5 Å, The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition.
8SGM 2.5 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
4EN3 2.57 Å, Crystal structure of a human Valpha24(-) NKT TCR in complex with…
4MQ7 2.6 Å, Structure of human CD1d-sulfatide
6V7Z 2.75 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
3U0P 2.8 Å, Crystal structure of human CD1d-lysophosphatidylcholine
8SGB 2.8 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
9O4X 2.86 Å, Gamma delta T cell receptor bound to CD1d

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