5MFD

Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.

Hansen, S.Kiefer, J.D.Madhurantakam, C.Mittl, P.R.E.Pluckthun, A.

(2017) Protein Sci 26: 1942-1952

  • DOI: https://doi.org/10.1002/pro.3229
  • Primary Citation of Related Structures:  
    5MFC, 5MFD

  • PubMed Abstract: 

    Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein-peptide interactions are characterized, and should always be correlated with measurements in solution.


  • Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YIIIM''6AII
A, C, E, G, I
A, C, E, G, I, J, K, L
328synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid decoration protein,pD_(KR)5
B, D, F, H
109Lambdavirus lambdaMutation(s): 0 
Gene Names: Dlambdap07
UniProt
Find proteins for P03712 (Escherichia phage lambda)
Explore P03712 
Go to UniProtKB:  P03712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03712
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth K]
BA [auth E]
BB [auth K]
CA [auth E]
AA [auth E],
AB [auth K],
BA [auth E],
BB [auth K],
CA [auth E],
CB [auth K],
DA [auth E],
DB [auth K],
EA [auth F],
EB [auth K],
FA [auth G],
FB [auth K],
GA [auth G],
GB [auth K],
HA [auth G],
HB [auth L],
IA [auth G],
IB [auth L],
JA [auth G],
KA [auth G],
LA [auth G],
M [auth A],
MA [auth G],
N [auth A],
NA [auth G],
O [auth A],
OA [auth H],
P [auth A],
PA [auth I],
Q [auth A],
QA [auth I],
R [auth A],
RA [auth I],
S [auth A],
SA [auth I],
T [auth A],
TA [auth J],
U [auth C],
UA [auth J],
V [auth E],
VA [auth J],
W [auth E],
WA [auth J],
X [auth E],
XA [auth K],
Y [auth E],
YA [auth K],
Z [auth E],
ZA [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.66α = 90
b = 194.66β = 90
c = 241.74γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description