6V7Z

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22

PDB DOI: https://doi.org/10.2210/pdb6V7Z/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252
R-Value Work: 0.186
R-Value Observed: 0.189

Starting Models: experimental
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This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 132.34 kDa
Atom Count: 7,908
Modelled Residue Count: 967
Deposited Residue Count: 1,130
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A, C	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15813
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P15813-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH ID22	E, F	118	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	G, J	2		N-Glycosylation	Interactions Focus chain G Focus chain J
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	H	2		N-Glycosylation	Interactions Focus chain H
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Entity ID: 6
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	I	3		N-Glycosylation	Interactions Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGH (Subject of Investigation/LOI) Query on AGH Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain R [auth C] mmCIF format, chain L [auth A] mmCIF format, chain R [auth C]	L [auth A], R [auth C]	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C₅₀ H₉₉ N O₉ VQFKFAKEUMHBLV-BYSUZVQFSA-N		Interactions Focus chain L [auth A] Focus chain R [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain Q [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain T [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth E]	M [auth A], N [auth A], T [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.717	α = 90
b = 121.933	β = 90
c = 172.136	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Shahine, A.

Rossjohn, J.

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary