6V7Z: Human CD1d presenting alpha-Galactosylceramide

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22. Determined by X-ray diffraction at 2.75 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 7,908
Mol. weight: 132.34 kDa
Ligands: AGH, NAG, BGC
Released: 16 Sept 2020

Explore 6V7Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V7Z contains 29 α-helices and 84 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 A: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
α-helix	47	1
β-strand	48-49	2	1
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	141-148	8
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-182	5
β-strand	185	1	2
β-strand	188-193	6	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	231-232	2	3
β-strand	236-237	2	3
β-strand	243-252	10	3
α-helix	253-256	4
β-strand	260-265	6	4
α-helix	266-268	3
β-strand	273-276	4	4

Chains B and D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
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 C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	8
β-strand	24-32	9	8
β-strand	35-40	6	8
β-strand	48-49	2	8
α-helix	60-87	28
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	8
β-strand	110-118	9	8
β-strand	121-127	7	8
β-strand	130-133	4	8
α-helix	140-148	9
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	9
β-strand	188-194	7	10
β-strand	203-211	9	10
β-strand	212	1	9
β-strand	216-222	7	11
β-strand	225-226	2	11
β-strand	231-232	2	10
β-strand	236-237	2	10
β-strand	243-250	8	10
β-strand	260-265	6	11
β-strand	273-276	4	11

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	10-12	3	16
β-strand	18-23	6	15
β-strand	31-39	9	16
β-strand	46-52	7	16
β-strand	57-59	3	16
α-helix	61-63	3
β-strand	64	1	15
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	87-89	3
β-strand	91-99	9	16
β-strand	102-108	7	16
β-strand	112-116	5	16

Chain F: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
β-strand	31-39	9	18
α-helix	44	1
β-strand	45-52	8	18
β-strand	57-59	3	18
β-strand	64	1	17
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-99	9	18
β-strand	107-108	2	18
β-strand	112-116	5	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A, C	protein	347	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Nanobody VHH ID22	E, F	protein	118	Lama glama

Sequence of entity 1 (A, C), FASTA

>6V7Z_1 Antigen-presenting glycoprotein CD1d (chains A, C)
MQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQW
ETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDI
LSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKK
QVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETW
YLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGSLVPRGSGSRIARLEEKVKTLKAQN
SELASTANMLREQVAQLKQKVMNHGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B, D), FASTA

>6V7Z_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, F), FASTA

>6V7Z_3 Nanobody VHH ID22 (chains E, F)
QVQLVESGGGLVQAGGSLRLSCAASGSIFSINAMGWYRQAPGKQRDFLAVISSSGSTNYA
DSVKGRFTISRDNAKNTAYLQMNSLKVEDTAVYYCAAHVAGFDEYNYWGQGTQVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
AGH	N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}h…	C50 H99 N O9	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
BGC	beta-D-glucopyranose	C6 H12 O6	1

Water and common crystallization additives (PEG, NA, 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
6V7Y 2.4 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
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
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

Browse structure collections

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