9LSW | pdb_00009lsw

Crystal structure of the calcium-free mRFP1 with a grafted calcium-binding sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 
    0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enhanced secretion through type 1 secretion system by grafting a calcium-binding sequence to modify the folding of cargo proteins.

Uehara, R.Kamiya, Y.Maeda, S.Okamoto, K.Toya, S.Chiba, R.Amesaka, H.Takano, K.Matsumura, H.Tanaka, S.I.

(2025) Protein Sci 34: e70165-e70165

  • DOI: https://doi.org/10.1002/pro.70165
  • Primary Citation of Related Structures:  
    9LSA, 9LSC, 9LSF, 9LSW

  • PubMed Abstract: 

    Extracellular secretion is a beneficial way to produce recombinant proteins at an industrial scale. Among bacterial secretion systems, the type 1 secretion system (T1SS) in Gram-negative bacteria is particularly attractive due to its simple architecture involving only three proteins and one-step translocation across both inner and outer membranes. However, proteins that fold rapidly within the cell often fail to pass through the narrow T1SS channel tunnel, limiting its industrial application. To address this limitation, we engineered a 10-amino-acid calcium-binding sequence (CBS) that disrupts proximal secondary structures through electrostatic repulsion at low Ca 2+ concentrations, thereby inhibiting premature folding of target proteins in the cell. We demonstrated that CBS-grafted variants of three fast-folding proteins-mRFP1, RNase H1, and monobody-were efficiently secreted by Escherichia coli expressing the Serratia marcescens Lip T1SS as compared to their parental proteins. Remarkably, the CBS-grafted variants were fully active and structurally identical to the intracellularly produced parental proteins when isolated from culture supernatants. Furthermore, the removal of Ca 2+ from CBS did not compromise the structure or function, indicating that the CBS-mediated calcium-dependent folding was irreversible. Our work will expand the utility of T1SS for secreting diverse proteins, paving the way for broader industrial applications.


  • Organizational Affiliation
    • Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Red fluorescent protein,grafted calcium-binding sequence
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
278Discosomasynthetic constructMutation(s): 1 
Gene Names: CH35J_004633
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.)
Explore Q9U6Y8 
Go to UniProtKB:  Q9U6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6Y8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRQ
Query on CRQ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.735α = 90
b = 132.276β = 90
c = 227.963γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21K05386
Japan Society for the Promotion of Science (JSPS)JapanJP23H04559
Japan Society for the Promotion of Science (JSPS)JapanJP24K08717

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary