7P2J

Dimethylated fusion protein of RSL and trimeric coiled coil (4dzn) in complex with cucurbit[7]uril, H3 sheet assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons.

Ramberg, K.O.Guagnini, F.Engilberge, S.Wronska, M.A.Rennie, M.L.Perez, J.Crowley, P.B.

(2021) Chemistry 27: 14619-14627

  • DOI: https://doi.org/10.1002/chem.202103025

  • PubMed Abstract: 

    One approach to protein assembly involves water-soluble supramolecular receptors that act like glues. Bionanoarchitectures directed by these scaffolds are often system-specific, with few studies investigating their customization. Herein, the modulation of cucurbituril-mediated protein assemblies through the inclusion of peptide tectons is described. Three peptides of varying length and structural order were N-terminally appended to RSL, a β-propeller building block. Each fusion protein was incorporated into crystalline architectures mediated by cucurbit[7]uril (Q7). A trimeric coiled-coil served as a spacer within a Q7-directed sheet assembly of RSL, giving rise to a layered material of varying porosity. Within the spacer layers, the coiled-coils were dynamic. This result prompted consideration of intrinsically disordered peptides (IDPs) as modulatory tectons. Similar to the coiled-coil, a mussel adhesion peptide (Mefp) also acted as a spacer between protein-Q7 sheets. In contrast, the fusion of a nucleoporin peptide (Nup) to RSL did not recapitulate the sheet assembly. Instead, a Q7-directed cage was adopted, within which disordered Nup peptides were partially "captured" by Q7 receptors. IDP capture occurred by macrocycle recognition of an intrapeptide Phe-Gly motif in which the benzyl group was encapsulated by Q7. The modularity of these protein-cucurbituril architectures adds a new dimension to macrocycle-mediated protein assembly. Segregated protein crystals, with alternating layers of high and low porosity, could provide a basis for new types of materials.


  • Organizational Affiliation

    School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin protein
A, B
114Ralstonia solanacearumMutation(s): 0 
Gene Names: E7Z57_08365HXP36_18875RSP795_21825RSP822_19650RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum)
Explore A0A0S4TLR1 
Go to UniProtKB:  A0A0S4TLR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TLR1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQ7 (Subject of Investigation/LOI)
Query on QQ7

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
cucurbit[7]uril
C42 H42 N28 O14
ZDOBFUIMGBWEAB-XGFHMVPTSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.617α = 90
b = 51.617β = 90
c = 322.633γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168
Science Foundation IrelandIrelandSSPC-PharM5 12/RC/2275_P2

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description