5TW5 | pdb_00005tw5

Structure of mouse CD1d with bound glycosphingolipid JJ112

PDB DOI: https://doi.org/10.2210/pdb5TW5/pdb

Classification: immune system/inhibitor
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2016-11-11 Released: 2017-09-20
Deposition Author(s): Zajonc, D.M., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.244 (Depositor), 0.252 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Galactosylsphingamides: new alpha-GalCer analogues to probe the F'-pocket of CD1d.

Guillaume, J., Wang, J., Janssens, J., Remesh, S.G., Risseeuw, M.D.P., Decruy, T., Froeyen, M., Elewaut, D., Zajonc, D.M., Calenbergh, S.V.

(2017) Sci Rep 7: 4276-4276

PubMed: 28655912 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-017-04461-7
Primary Citation Related Structures:
5TW2, 5TW5

PubMed Abstract:
Invariant Natural Killer T-cells (iNKT-cells) are an attractive target for immune response modulation, as upon CD1d-mediated stimulation with KRN7000, a synthetic α-galactosylceramide, they produce a vast amount of cytokines. Here we present a synthesis that allows swift modification of the phytosphingosine side chain by amidation of an advanced methyl ester precursor. The resulting KRN7000 derivatives, termed α-galactosylsphingamides, were evaluated for their capacity to stimulate iNKT-cells. While introduction of the amide-motif in the phytosphingosine chain is tolerated for CD1d binding and TCR recognition, the studied α-galactosylsphingamides showed compromised antigenic properties.

Organizational Affiliation

Laboratory for Medicinal Chemistry (FFW), Faculty of Pharmaceutical Sciences, UGent, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.

Macromolecule Content

Total Structure Weight: 45.82 kDa
Atom Count: 3,438
Modeled Residue Count: 369
Deposited Residue Count: 382
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A	285	Mus musculus	Mutation(s): 1 Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609 Go to UniProtKB: P11609
IMPC: MGI:107674
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11609
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P11609-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	97	Mus musculus	Mutation(s): 0 Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7LM Query on 7LM Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide C₃₆ H₆₃ N O₉ YDGPBAWHWVHKQP-QNAIHFNASA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.244 (Depositor), 0.252 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.172	α = 90
b = 106.231	β = 90
c = 106.892	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Blue	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Zajonc, D.M.

Wang, J.

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary