6FOF

Crystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/VII-IX]

PDB DOI: https://doi.org/10.2210/pdb6FOF/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-07 Released: 2018-07-18
Deposition Author(s): Romero, A., Flores-Ibarra, A., Medrano, F.J.
Funding Organization(s): Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.264
R-Value Work: 0.213

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystallization of a human galectin-3 variant with two ordered segments in the shortened N-terminal tail.

Flores-Ibarra, A., Vertesy, S., Medrano, F.J., Gabius, H.J., Romero, A.

(2018) Sci Rep 8: 9835-9835

PubMed: 29959397 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-018-28235-x
Primary Citation of Related Structures:
6FOF

PubMed Abstract:
Among members of the family of adhesion/growth-regulatory galectins, galectin-3 (Gal-3) bears a unique modular architecture. A N-terminal tail (NT) consisting of the N-terminal segment (NTS) and nine collagen-like repeats is linked to the canonical lectin domain. In contrast to bivalent proto- and tandem-repeat-type galectins, Gal-3 is monomeric in solution, capable to self-associate in the presence of bi- to multivalent ligands, and the NTS is involved in cellular compartmentalization. Since no crystallographic information on Gal-3 beyond the lectin domain is available, we used a shortened variant with NTS and repeats VII-IX. This protein crystallized as tetramers with contacts between the lectin domains. The region from Tyr101 (in repeat IX) to Leu114 (in the CRD) formed a hairpin. The NTS extends the canonical β-sheet of F1-F5 strands with two new β-strands on the F face. Together, crystallographic and SAXS data reveal a mode of intramolecular structure building involving the highly flexible Gal-3's NT.

Organizational Affiliation

Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.

Macromolecule Content

Total Structure Weight: 260.93 kDa
Atom Count: 14,090
Modelled Residue Count: 1,696
Deposited Residue Count: 2,352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3,Galectin-3	A [auth C] B [auth D] C [auth E] D [auth G] E [auth A] A [auth C], B [auth D], C [auth E], D [auth G], E [auth A], F [auth B], G [auth F], H, I, J, K, L	196	Homo sapiens	Mutation(s): 0 Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens) Explore P17931 Go to UniProtKB: P17931
PHAROS: P17931 GTEx: ENSG00000131981
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17931
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	2		N/A	Interactions Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth F] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain OA [auth H] SDF format, chain PA [auth I] SDF format, chain QA [auth I] SDF format, chain RA [auth J] SDF format, chain SA [auth K] SDF format, chain TA [auth K] SDF format, chain UA [auth K] SDF format, chain VA [auth L] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain RA [auth J] MOL2 format, chain SA [auth K] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth K] MOL2 format, chain VA [auth L] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain MA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth I] mmCIF format, chain QA [auth I] mmCIF format, chain RA [auth J] mmCIF format, chain SA [auth K] mmCIF format, chain TA [auth K] mmCIF format, chain UA [auth K] mmCIF format, chain VA [auth L] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth D] DA [auth D] EA [auth E] AA [auth C], BA [auth C], CA [auth D], DA [auth D], EA [auth E], FA [auth G], GA [auth G], HA [auth G], IA [auth B], JA [auth B], KA [auth F], LA [auth H], MA [auth H], NA [auth H], OA [auth H], PA [auth I], QA [auth I], RA [auth J], SA [auth K], TA [auth K], UA [auth K], VA [auth L], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth E] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth F] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain RA [auth J] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain VA [auth L] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth E] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth F] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain RA [auth J] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth K] Focus chain VA [auth L] Focus chain Y [auth C] Focus chain Z [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	M, N, O, P, Q M, N, O, P, Q, R, S, T, U, V, W, X	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.264
R-Value Work: 0.213
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.851	α = 90
b = 98.195	β = 90
c = 237.814	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Romero, A.

Flores-Ibarra, A.

Medrano, F.J.

Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness	Spain	BFU2016-77835-R

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary