6EKE

crystal structure of a Pholiota squarrosa lectin unliganded

PDB DOI: https://doi.org/10.2210/pdb6EKE/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pholiota squarrosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-26 Released: 2018-07-11
Deposition Author(s): Cabanettes, A., Varrot, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.211
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin.

Cabanettes, A., Perkams, L., Spies, C., Unverzagt, C., Varrot, A.

(2018) Angew Chem Int Ed Engl 57: 10178-10181

PubMed: 29956878 Search on PubMed
DOI: https://doi.org/10.1002/anie.201805165
Primary Citation of Related Structures:
6EKE, 6FX1, 6FX2, 6FX3

PubMed Abstract:
The mini fungal lectin PhoSL was recombinantly produced and characterized. Despite a length of only 40 amino acids, PhoSL exclusively recognizes N-glycans with α1,6-linked fucose. Core fucosylation influences the intrinsic properties and bioactivities of mammalian N-glycoproteins and its level is linked to various cancers. Thus, PhoSL serves as a promising tool for glycoprofiling. Without structural precedence, the crystal structure was solved using the zinc anomalous signal, and revealed an interlaced trimer creating a novel protein fold termed β-prism III. Three biantennary core-fucosylated N-glycan azides of 8 to 12 sugars were cocrystallized with PhoSL. The resulting highly resolved structures gave a detailed view on how the exclusive recognition of α1,6-fucosylated N-glycans by such a small protein occurs. This work also provided a protein consensus motif for the observed specificity as well as a glimpse into N-glycan flexibility upon binding.

Organizational Affiliation

Univ. Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 14.88 kDa
Atom Count: 1,113
Modelled Residue Count: 116
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lectin	A, B [auth C], C [auth B]	43	Pholiota squarrosa	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEU4 (Pholiota squarrosa) Explore A0A3B6UEU4 Go to UniProtKB: A0A3B6UEU4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3B6UEU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B]	F [auth A], N [auth B]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth C]	D [auth A], G [auth A], I [auth A], J [auth C], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth C] Focus chain M [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	E [auth A], H [auth A], K [auth C], L [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain L [auth C]