3S64 | pdb_00003s64

Saposin-like protein Ac-SLP-1

PDB DOI: https://doi.org/10.2210/pdb3S64/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Ancylostoma caninum
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2011-05-25 Released: 2012-01-18
Deposition Author(s): Willis, C., Wang, C.K., Osman, A., Simon, A., Mulvenna, J., Pickering, D., Riboldi-Tunicliffe, A., Jones, M.K., Loukas, A., Hofmann, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.252 (Depositor), 0.253 (DCC)
R-Value Work:
0.225 (Depositor), 0.233 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Insights into the membrane interactions of the saposin-like proteins Na-SLP-1 and Ac-SLP-1 from human and dog hookworm.

Willis, C., Wang, C.K., Osman, A., Simon, A., Pickering, D., Mulvenna, J., Riboldi-Tunicliffe, A., Jones, M.K., Loukas, A., Hofmann, A.

(2011) PLoS One 6: e25369-e25369

PubMed: 21991310 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0025369
Primary Citation Related Structures:
3S63, 3S64

PubMed Abstract:
Saposin-like proteins (SAPLIPs) from soil-transmitted helminths play pivotal roles in host-pathogen interactions and have a high potential as targets for vaccination against parasitic diseases. We have identified two non-orthologous SAPLIPs from human and dog hookworm, Na-SLP-1 and Ac-SLP-1, and solved their three-dimensional crystal structures. Both proteins share the property of membrane binding as monitored by liposome co-pelleting assays and monolayer adsorption. Neither SAPLIP displayed any significant haemolytic or bactericidal activity. Based on the structural information, as well as the results from monolayer adsorption, we propose models of membrane interactions for both SAPLIPs. Initial membrane contact of the monomeric Na-SLP-1 is most likely by electrostatic interactions between the membrane surface and a prominent basic surface patch. In case of the dimeric Ac-SLP-1, membrane interactions are most likely initiated by a unique tryptophan residue that has previously been implicated in membrane interactions in other SAPLIPs.

Organizational Affiliation

Parasite Cell Biology, Queensland Institute of Medical Research, Herston, Queensland, Australia.

Macromolecule Content

Total Structure Weight: 9.97 kDa
Atom Count: 666
Modeled Residue Count: 81
Deposited Residue Count: 87
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saposin-like protein 1	A	87	Ancylostoma caninum	Mutation(s): 0 Gene Names: SLP1
UniProt
Find proteins for Q0MRQ4 (Ancylostoma caninum) Explore Q0MRQ4 Go to UniProtKB: Q0MRQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0MRQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252 (Depositor), 0.253 (DCC)
R-Value Work: 0.225 (Depositor), 0.233 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.053	α = 90
b = 72.053	β = 90
c = 90.888	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Riboldi-Tunicliffe, A.

Jones, M.K.

Loukas, A.

Hofmann, A.

Revision History (Full details and data files)

Version 1.0: 2012-01-18
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary