9LKI | pdb_00009lki

N-terminal domain (NTD) structure of aciniform spidroin 1(AcSp1) from Latrodectus hesperus

• PDB DOI: https://doi.org/10.2210/pdb9LKI/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Latrodectus hesperus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-16 Released: 2025-10-01 
• Deposition Author(s): Yang, R., Qin, R., Yuan, W., Lin, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.322 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.286 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

Starting Model: in silico

Literature

The self-assemble of N-terminal domain of aciniform spidroin 1 (AcSp1) from Latrodectus hesperus

Yang, R., Qin, R., Yuan, W., Lin, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.29 kDa 
• Atom Count: 3,775 
• Modeled Residue Count: 500 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aciniform spidroin 1	A [auth D], B [auth C], C [auth A], D [auth B]	144	Latrodectus hesperus	Mutation(s): 0  Gene Names: AcSp1
UniProt
Find proteins for K7YP04 (Latrodectus hesperus) Explore K7YP04  Go to UniProtKB:  K7YP04

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.322 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.286 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.62	α = 90
b = 82.34	β = 94.163
c = 65.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Yang, R., Qin, R., Yuan, W., Lin, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release