1OUW | pdb_00001ouw

Crystal structure of Calystegia sepium agglutinin

PDB DOI: https://doi.org/10.2210/pdb1OUW/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Calystegia sepium
Mutation(s): Yes

Deposited: 2003-03-25 Released: 2003-11-11
Deposition Author(s): Bourne, Y., Roig-Zamboni, V., Barre, A., Peumans, W.J., Astoul, C.H., van Damme, E.J.M., Rouge, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.180 (Depositor), 0.223 (DCC)
R-Value Work:
0.153 (Depositor)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of the Calystegia sepium agglutinin reveals a novel quaternary arrangement of lectin subunits with a beta-prism fold

Bourne, Y., Roig-Zamboni, V., Barre, A., Peumans, W.J., Astoul, C.H., Van Damme, E.J.M., Rouge, P.

(2004) J Biological Chem 279: 527-533

PubMed: 14561768 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M308218200
Primary Citation Related Structures:
1OUW

PubMed Abstract:
The high number of quaternary structures observed for lectins highlights the important role of these oligomeric assemblies during carbohydrate recognition events. Although a large diversity in the mode of association of lectin subunits is frequently observed, the oligomeric assemblies of plant lectins display small variations within a single family. The crystal structure of the mannose-binding jacalin-related lectin from Calystegia sepium (Calsepa) has been determined at 1.37-A resolution. Calsepa exhibits the same beta-prism fold as identified previously for other members of the family, but the shape and the hydrophobic character of its carbohydrate-binding site is unlike that of other members, consistent with surface plasmon resonance analysis showing a preference for methylated sugars. Calsepa reveals a novel dimeric assembly markedly dissimilar to those described earlier for Heltuba and jacalin but mimics the canonical 12-stranded beta-sandwich dimer found in legume lectins. The present structure exemplifies the adaptability of the beta-prism building block in the evolution of plant lectins and highlights the biological role of these quaternary structures for carbohydrate recognition.

Organizational Affiliation

AFMB-CNRS, CNRS UMR6098, F13402 Marseille Cedex 20, France. yves@afmb.cnrs-mrs.fr

Macromolecule Content

Total Structure Weight: 65.05 kDa
Atom Count: 5,125
Modeled Residue Count: 602
Deposited Residue Count: 608
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	152	Calystegia sepium	Mutation(s): 1
UniProt
Find proteins for P93114 (Calystegia sepium) Explore P93114 Go to UniProtKB: P93114
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P93114
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	N [auth C], Q [auth D]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain N [auth C] Focus chain Q [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], H [auth A], L [auth B], M [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], O [auth C], P [auth C], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AYA Query on AYA	A, B, C, D	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.180 (Depositor), 0.223 (DCC)
R-Value Work: 0.153 (Depositor)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.562	α = 104.99
b = 51.792	β = 94.36
c = 79.78	γ = 94.85

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-11
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary