8YT7 | pdb_00008yt7

Crystal structure of the MAM domain of Spodoptera frugiperda Scavenger Receptor-C

• PDB DOI: https://doi.org/10.2210/pdb8YT7/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-03-25 Released: 2025-04-02 
• Deposition Author(s): Lan, J., Wang, C.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Binding Analysis of Sf-SR-C MAM Domain and Sf-FGFR Ectodomain to Vip3Aa.

Wang, C., Li, M., Chen, X., Fan, S., Lan, J.

(2024) Insects 15

• PubMed: 38921143 
• DOI: https://doi.org/10.3390/insects15060428
• Primary Citation of Related Structures:  
  8YT7


• PubMed Abstract: 
  

  Bacillus thuringiensis Vip3Aa has been widely used in transgenic crops to resist the erosion of insects. The Scavenger Receptor-C (SR-C) and Fibroblast Growth Factor Receptor (FGFR) of Spodoptera frugiperda (Sf-SR-C and Sf-FGFR) have formerly been identified as the cell receptors of Vip3Aa. However, the interaction mechanism of Vip3Aa binding to Sf-SR-C or Sf-FGFR is still unknown. Here, we purified the MAM domain of Sf-SR-C (Sf-MAM) and the Sf-FGFR ectodomain expressed extracellularly by Sf9 cells. We then solved the crystal structure of the Sf-MAM domain. Structure docking analysis of the Sf-MAM and Vip3Aa C-terminal domain (CTD) excluded the possibility of the two proteins binding. A further surface plasmon resonance (SPR) assay also revealed that the Sf-MAM and Sf-FGFR ectodomain could not bind to the Vip3Aa protein. Our results have raised the urgency of determining the authentic cell receptor for Vip3Aa.

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Organizational Affiliation: 
• School of Biomedical Sciences, Hunan University, Changsha 410082, China.
Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.43 kDa 
• Atom Count: 1,577 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor SR-C-like protein	A	189	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for A0S6A2 (Spodoptera frugiperda) Explore A0S6A2  Go to UniProtKB:  A0S6A2
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.02	α = 90
b = 57.02	β = 90
c = 159.934	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Lan, J., Wang, C.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Database references