7P2I | pdb_00007p2i

Dimethylated fusion protein of RSL and nucleoporin peptide (Nup) in complex with cucurbit[7]uril, F432 cage assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.178 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
  • Primary Citation Related Structures: 
    6S99, 7P2H, 7P2I, 7P2J

  • 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.

Macromolecule Content 

  • Total Structure Weight: 36.62 kDa 
  • Atom Count: 2,809 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fucose-binding lectin protein
A, B, C
102Ralstonia 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQ7
(Subject of Investigation/LOI)

Query on QQ7



Download:Ideal Coordinates CCD File
F [auth A],
K [auth C]
cucurbit[7]uril
C42 H42 N28 O14
ZDOBFUIMGBWEAB-XGFHMVPTSA-N
MFU

Query on MFU



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
G [auth B]
H [auth B]
I [auth C]
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth C],
J [auth C]
methyl alpha-L-fucopyranoside
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C
L-PEPTIDE LINKINGC8 H18 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.178 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.713α = 90
b = 200.713β = 90
c = 200.713γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

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
Irish Research CouncilIrelandGOIPD/2019/513

Revision History  (Full details and data files)

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