6V7Y

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5

• PDB DOI: https://doi.org/10.2210/pdb6V7Y/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-10 Released: 2020-09-16 
• Deposition Author(s): Shahine, A., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.241 
• R-Value Observed: 0.201 

Literature

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.

Shahine, A., Rossjohn, J.

(2020) Nat Cancer 

• DOI: https://doi.org/10.1038/s43018-020-00111-6

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 68.11 kDa 
• Atom Count: 4,324 
• Modelled Residue Count: 496 
• Deposited Residue Count: 574 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A	347	Homo sapiens	Mutation(s): 0  Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813
PHAROS:  P15813 GTEx:  ENSG00000158473

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH ID5	C [auth F]	127	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGH (Subject of Investigation/LOI)	H [auth A]	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C50 H99 N O9 VQFKFAKEUMHBLV-BYSUZVQFSA-N
NAG	F [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	G [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	J [auth A], K [auth A], L [auth A], M [auth A], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.241 
• R-Value Observed: 0.201 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.27	α = 90
b = 73.27	β = 90
c = 261.077	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 6V7Y does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Shahine, A., Rossjohn, J.

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description