5LEL

Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_10_3G124 in complex with Maltose-binding Protein and Green Fluorescent Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rigidly connected multispecific artificial binders with adjustable geometries.

Wu, Y.Batyuk, A.Honegger, A.Brandl, F.Mittl, P.R.E.Pluckthun, A.

(2017) Sci Rep 7: 11217-11217

  • DOI: 10.1038/s41598-017-11472-x
  • Primary Citation of Related Structures:  
    5LEM, 5LEL, 5LEA, 5LEC, 5LEB, 5LEE, 5LED, 5LE7, 5LE6, 5LE9

  • PubMed Abstract: 
  • Multivalent binding proteins can gain biological activities beyond what is inherent in the individual binders, by bringing together different target molecules, restricting their conformational flexibility or changing their subcellular localization. I ...

    Multivalent binding proteins can gain biological activities beyond what is inherent in the individual binders, by bringing together different target molecules, restricting their conformational flexibility or changing their subcellular localization. In this study, we demonstrate a method to build up rigid multivalent and multispecific scaffolds by exploiting the modular nature of a repeat protein scaffold and avoiding flexible linkers. We use DARPins (Designed Ankyrin Repeat Proteins), synthetic binding proteins based on the Ankyrin-repeat protein scaffold, as binding units. Their ease of in vitro selection, high production yield and stability make them ideal specificity-conferring building blocks for the design of more complex constructs. C- and N-terminal DARPin capping repeats were re-designed to be joined by a shared helix in such a way that rigid connector modules are formed. This allows us to join two or more DARPins in predefined geometries without compromising their binding affinities and specificities. Nine connector modules with distinct geometries were designed; for eight of these we were able to confirm the structure by X-ray crystallography, while only one did not crystallize. The bispecific constructs were all able to bind both target proteins simultaneously.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland. plueckthun@bioc.uzh.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DD_Off7_10_3G124ADG325synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinBEH395Escherichia coli K-12Mutation(s): 0 
Gene Names: malEZ5632ECs5017
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinCFI247Aequorea victoriaMutation(s): 2 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
C,F,IL-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235α = 90
b = 103.14β = 131.35
c = 156.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_166676
European Research CouncilNEXTBINDERS

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection