8CF7

Dimethylated RSL-R5 in complex with cucurbit[7]uril, C121 sheet assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Cage versus sheet: Probing the Determinants of Protein - Cucurbit[7]uril Crystalline Architectures.

Ramberg, K.O.Crowley, P.B.

(2023) J Struct Biol 215: 107969-107969

  • DOI: https://doi.org/10.1016/j.jsb.2023.107969
  • Primary Citation of Related Structures:  
    8CF6, 8CF7

  • PubMed Abstract: 

    The donut-shaped cucurbit[n]urils (Qn) are a class of rigid macrocyclic receptor with protein recognition capabilities. Qn encapsulation of amino acid side chains can enable protein assembly. Recently, cucurbit[7]uril (Q7) has been applied as a molecular glue for organizing protein building blocks into crystalline architectures. Q7 co-crystallization with dimethylated Ralstonia solanacearum lectin (RSL*) has yielded novel crystalline architectures. Co-crystallization of RSL* and Q7 yields either cage- or sheet-like architectures which may be modulated via protein engineering. However, questions remain as to the factors dictating the formation of one architecture over another (cage versus sheet). Here, we make use of an engineered RSL*-Q7 system which co-crystallizes as the cage or sheet assembly with easily-distinguished crystal morphologies. Using this model system, we probe how the crystallization conditions dictate which crystalline architecture is adopted. Protein-ligand ratios and the sodium concentration were identified as key determinants for the growth of the cage versus sheet assemblies.


  • Organizational Affiliation

    School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland. Electronic address: rambergk@tcd.ie.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RSL-R5
A, B, C, D, E
A, B, C, D, E, F
90Ralstonia solanacearumMutation(s): 0 
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 
G [auth A]
K [auth B]
O [auth C]
R [auth D]
V [auth E]
G [auth A],
K [auth B],
O [auth C],
R [auth D],
V [auth E],
Z [auth F]
cucurbit[7]uril
C42 H42 N28 O14
ZDOBFUIMGBWEAB-XGFHMVPTSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
H [auth A]
I [auth A]
AA [auth F],
BA [auth F],
CA [auth F],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
W [auth E],
X [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.695α = 90
b = 50.396β = 90.05
c = 140.219γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
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 IrelandIrelandand 12/RC/2275_P2

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release