7P4T | pdb_00007p4t

Tetrameric structure of murine SapA

• PDB DOI: https://doi.org/10.2210/pdb7P4T/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-13 Released: 2022-05-25 
• Deposition Author(s): Shamin, M., Deane, J.E.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.304 (Depositor) 
• R-Value Work: 
  0.272 (Depositor), 0.276 (DCC) 

Starting Model: experimental

Literature

A Tetrameric Assembly of Saposin A: Increasing Structural Diversity in Lipid Transfer Proteins.

Shamin, M., Spratley, S.J., Graham, S.C., Deane, J.E.

(2021) Contact (Thousand Oaks) 4: 251525642110523-251525642110523

• PubMed: 37143956 
• DOI: https://doi.org/10.1177/25152564211052382
• Primary Citation Related Structures: 
  7P4T


• PubMed Abstract: 
  

  Saposins are lipid transfer proteins required for the degradation of sphingolipids in the lysosome. These small proteins bind lipids by transitioning from a closed, monomeric state to an open conformation exposing a hydrophobic surface that binds and shields hydrophobic lipid tails from the aqueous environment. Saposins form a range of multimeric assemblies to encompass these bound lipids and present them to hydrolases in the lysosome. This lipid-binding property of human saposin A has been exploited to form lipoprotein nanodiscs suitable for structural studies of membrane proteins. Here we present the crystal structure of a unique tetrameric assembly of murine saposin A produced serendipitously, following modifications of published protocols for making lipoprotein nanodiscs. The structure of this new saposin oligomer highlights the diversity of tertiary arrangement that can be adopted by these important lipid transfer proteins.

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Organizational Affiliation: 
• Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 36.49 kDa 
• Atom Count: 2,432 
• Modeled Residue Count: 320 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saposin-A	A, B, C, D	83	Mus musculus	Mutation(s): 0  Gene Names: Psap, Sgp1
UniProt
Find proteins for Q61207 (Mus musculus) Explore Q61207  Go to UniProtKB:  Q61207

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.304 (Depositor) 
• R-Value Work:  0.272 (Depositor), 0.276 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.489	α = 90
b = 48.489	β = 90
c = 314.359	γ = 120

Software Package:

Software Name	Purpose
DIALS	data collection
autoPROC	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Shamin, M., Deane, J.E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2023-05-17
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary