3T8X | pdb_00003t8x

Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer

PDB DOI: https://doi.org/10.2210/pdb3T8X/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Mus musculus
Mutation(s): No

Deposited: 2011-08-02 Released: 2011-10-26
Deposition Author(s): Garcia-Alles, L.F., Maveyraud, L., Mourey, L., Julien, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.165 (Depositor), 0.173 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural reorganization of the human CD1b Antigen-binding groove for presentation of mycobacterial sulfoglycolipids

Garcia-Alles, L.F., Collmann, A., Versluis, C., Lindner, B., Guiard, J., Maveyraud, L., Huc, E., Im, J.S., Sansano, S., Brando, T., Julien, S., Prandi, J., Gilleron, M., Porcelli, S.A., de la Salle, H., Heck, A.J.R., Mori, L., Puzo, G., Mourey, L., De Libero, G.

To be published.

Macromolecule Content

Total Structure Weight: 96.73 kDa
Atom Count: 6,803
Modeled Residue Count: 750
Deposited Residue Count: 800
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1b	A, C	301	Homo sapiens	Mutation(s): 0 Gene Names: CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens) Explore P29016 Go to UniProtKB: P29016
PHAROS: P29016 GTEx: ENSG00000158485
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29016
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P29016-1
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, D	99	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	5		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T8X Query on T8X Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C]	K [auth A], Q [auth C]	2-O-sulfo-alpha-D-glucopyranosyl 2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-tetramethyltetracos-2-enoyl]-alpha-D-glucopyranoside C₅₆ H₁₀₄ O₁₆ S NEVRXHPVRYSQOZ-ZZLYBKFXSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth C] Interactions & Density Focus chain K [auth A] Focus chain Q [auth C]
ULI Query on ULI 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]	tetracontane C₄₀ H₈₂ KUPLEGDPSCCPJI-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain R [auth C] Interactions & Density Focus chain L [auth A] Focus chain R [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain P [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C]	I [auth A], O [auth C], P [auth C], S [auth D], T [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth D]	M [auth B], N [auth B], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth D] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.165 (Depositor), 0.173 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.25	α = 90
b = 67.58	β = 112.26
c = 88.19	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary