5M62 | pdb_00005m62

Structure of the Mus musclus Langerin carbohydrate recognition domain in complex with glucose

• PDB DOI: https://doi.org/10.2210/pdb5M62/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-24 Released: 2016-12-07 
• Deposition Author(s): Loll, B., Aretz, J., Rademacher, C., Wahl, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.164 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.144 (Depositor) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Bacterial Polysaccharide Specificity of the Pattern Recognition Receptor Langerin Is Highly Species-dependent.

Hanske, J., Schulze, J., Aretz, J., McBride, R., Loll, B., Schmidt, H., Knirel, Y., Rabsch, W., Wahl, M.C., Paulson, J.C., Rademacher, C.

(2017) J Biological Chem 292: 862-871

• PubMed: 27903635 
• DOI: https://doi.org/10.1074/jbc.M116.751750
• Primary Citation Related Structures: 
  5K8Y, 5M62


• PubMed Abstract: 
  

  The recognition of pathogen surface polysaccharides by glycan-binding proteins is a cornerstone of innate host defense. Many members of the C-type lectin receptor family serve as pattern recognition receptors facilitating pathogen uptake, antigen processing, and immunomodulation. Despite the high evolutionary pressure in host-pathogen interactions, it is still widely assumed that genetic homology conveys similar specificities. Here, we investigate the ligand specificities of the human and murine forms of the myeloid C-type lectin receptor langerin for simple and complex ligands augmented by structural insight into murine langerin. Although the two homologs share the same three-dimensional structure and recognize simple ligands identically, a screening of more than 300 bacterial polysaccharides revealed highly diverging avidity and selectivity for larger and more complex glycans. Structural and evolutionary conservation analysis identified a highly variable surface adjacent to the canonic binding site, potentially forming a secondary site of interaction for large glycans.

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Organizational Affiliation: 
• From the Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany.
the Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin 14195, Germany.
the Department of Cell and Molecular Biology, Department of Immunology and Microbial Science and Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037.
the N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia, and.
the Robert Koch Institute, Wernigerode Branch, National Reference Centre for Salmonellae and other Bacterial Enteric Pathogens, Wernigerode 38855, Germany.
From the Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany, [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2,722 
• Modeled Residue Count: 272 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member K	A, B	151	Mus musculus	Mutation(s): 1  Gene Names: Cd207, Clec4k
UniProt
Find proteins for Q8VBX4 (Mus musculus) Explore Q8VBX4  Go to UniProtKB:  Q8VBX4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	J [auth A], Q [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
GLC	O [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
BGC	K [auth A], P [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.164 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.144 (Depositor) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.42	α = 90
b = 144.42	β = 90
c = 144.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Loll, B., Aretz, J., Rademacher, C., Wahl, M.C.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references
• Version 1.2: 2017-02-01
  Changes: Database references
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2019-10-30
  Changes: Data collection, Structure summary
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.7: 2024-11-13
  Changes: Structure summary