6FX1 | pdb_00006fx1

Crystal structure of Pholiota squarrosa lectin in complex with an octasaccharide

PDB DOI: https://doi.org/10.2210/pdb6FX1/pdb

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

Deposited: 2018-03-08 Released: 2018-07-11
Deposition Author(s): Cabanettes, A., Varrot, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.186 (Depositor)

Starting Model: other
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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

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 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: 71.15 kDa
Atom Count: 5,109
Modeled Residue Count: 487
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lectin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	43	Pholiota squarrosa	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEU4 (Pholiota squarrosa) Explore A0A3B6UEU4 Go to UniProtKB: A0A3B6UEU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3B6UEU4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine	M, O, R, X	6	N/A	N/A	Interactions Focus chain M Focus chain O Focus chain R Focus chain X Interactions & Density Focus chain M Focus chain O Focus chain R Focus chain X
Glycosylation Resources
GlyTouCan: G53233QZ GlyCosmos: G53233QZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine	N, U	8	N/A	N/A	Interactions Focus chain N Focus chain U Interactions & Density Focus chain N Focus chain U
Glycosylation Resources
GlyTouCan: G12228DK GlyCosmos: G12228DK

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine	P	5	N/A	N/A	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G15526KS GlyCosmos: G15526KS

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine	Q, S	7	N/A	N/A	Interactions Focus chain Q Focus chain S Interactions & Density Focus chain Q Focus chain S
Glycosylation Resources
GlyTouCan: G70122IR GlyCosmos: G70122IR

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]1-azido-beta-N-acetyl-D-glucosamine	T, V, W	4	N/A	N/A	Interactions Focus chain T Focus chain V Focus chain W Interactions & Density Focus chain T Focus chain V Focus chain W
Glycosylation Resources
GlyTouCan: G02611HY GlyCosmos: G02611HY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OOA Query on OOA Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain Z [auth A]	Z [auth A]	3-OXOOCTANOIC ACID C₈ H₁₄ O₃ FWNRRWJFOZIGQZ-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Interactions & Density Focus chain Z [auth A]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain KA [auth K] SDF format, chain JA [auth I] SDF format, chain IA [auth H] SDF format, chain HA [auth H] SDF format, chain GA [auth F] SDF format, chain FA [auth E] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain KA [auth K] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain KA [auth K] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth C] CA [auth D] DA [auth D] EA [auth D] AA [auth B], BA [auth C], CA [auth D], DA [auth D], EA [auth D], FA [auth E], GA [auth F], HA [auth H], IA [auth H], JA [auth I], KA [auth K], Y [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth I] Focus chain KA [auth K] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth I] Focus chain KA [auth K] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.219 (Depositor)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91	α = 90
b = 95.593	β = 90
c = 110.633	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Cabanettes, A.

Varrot, A.

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 1.1: 2018-07-18
Changes: Data collection, Structure summary
Version 1.2: 2018-08-29
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary