9HRZ | pdb_00009hrz

The RSL-R6 - pctx complex, H3 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Protein Recognition and Assembly by a Phosphocavitand.

Wren, C.P.Flood, R.J.Mockler, N.M.Savko, M.Malinska, M.Shi, Q.Crowley, P.B.

(2025) J Am Chem Soc 147: 28107-28116

  • DOI: https://doi.org/10.1021/jacs.5c08121
  • Primary Citation Related Structures: 
    9HRU, 9HRV, 9HRW, 9HRX, 9HRY, 9HRZ

  • PubMed Abstract: 

    Controlled protein assembly is an enabling technology, in particular, for biomaterials fabrication. Here, we report protein recognition and assembly by a phosphate-containing macrocycle ( pctx ). We show that the C 3 -symmetric phosphocavitand is a versatile receptor for N-terminal residues or arginine but not lysine. Using atomic resolution X-ray diffraction data, we reveal the precise details of N-terminal complexation in the β-propeller protein Ralstonia solanacearum lectin (RSL). In some cocrystal structures, a tetrahedral cluster of the phosphocavitand occupies one end of the β-propeller fold, providing a node for protein assembly. The macrocycle cluster is compatible with different types of precipitants, a broad pH range, and zinc complexation. We demonstrate system control with an arginine-enriched RSL that alters the overall assembly due to selective arginine complexation by pctx . A lysozyme- pctx cocrystal structure also demonstrates arginine complexation by the macrocycle. An alternative macrocycle cluster occurs with an engineered RSL bearing an extended N-terminus. In this structure, involving zinc ligation at the N-terminus, the macrocycle forms trimeric clusters and four such clusters form cage-like substructures within the tetrahedral protein framework. Thus, N-terminal complexation in combination with phosphocavitand self-assembly provides new routes to protein crystal engineering.


  • Organizational Affiliation
    • School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland.

Macromolecule Content 

  • Total Structure Weight: 11.45 kDa 
  • Atom Count: 926 
  • Modeled Residue Count: 90 
  • Deposited Residue Count: 90 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucose-binding lectin protein90Ralstonia solanacearumMutation(s): 3 
Gene Names: E7Z57_08365RSP795_21825RSP822_19650RUN39_v1_50103
UniProt
Find proteins for A0AAP7ZHZ3 (Ralstonia solanacearum K60)
Explore A0AAP7ZHZ3 
Go to UniProtKB:  A0AAP7ZHZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAP7ZHZ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.569α = 90
b = 43.569β = 90
c = 122.997γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/RC/2275_P2

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release