7Q5G

LAN-DAP5 DERIVATIVE OF LANREOTIDE: L-DIAMINO PROPIONIC ACID IN POSITION 5 IN PLACE OF L-LYSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.086 
  • R-Value Work: 0.077 
  • R-Value Observed: 0.078 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Atomic structure of Lanreotide nanotubes revealed by cryo-EM.

Pieri, L.Wang, F.Arteni, A.A.Vos, M.Winter, J.M.Le Du, M.H.Artzner, F.Gobeaux, F.Legrand, P.Boulard, Y.Bressanelli, S.Egelman, E.H.Paternostre, M.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2120346119
  • Primary Citation of Related Structures:  
    7Q5A, 7Q5G

  • PubMed Abstract: 

    Functional and versatile nano- and microassemblies formed by biological molecules are found at all levels of life, from cell organelles to full organisms. Understanding the chemical and physicochemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes they carry out but also to mimic nature. Among the synthetic peptides forming well-defined nanostructures, the octapeptide Lanreotide has been considered one of the best characterized, in terms of both the atomic structure and its self-assembly process. In the present work, we determined the atomic structure of Lanreotide nanotubes at 2.5-Å resolution by cryoelectron microscopy (cryo-EM). Surprisingly, the asymmetric unit in the nanotube contains eight copies of the peptide, forming two tetramers. There are thus eight different environments for the peptide, and eight different conformations in the nanotube. The structure built from the cryo-EM map is strikingly different from the molecular model, largely based on X-ray fiber diffraction, proposed 20 y ago. Comparison of the nanotube with a crystal structure at 0.83-Å resolution of a Lanreotide derivative highlights the polymorphism for this peptide family. This work shows once again that higher-order assemblies formed by even well-characterized small peptides are very difficult to predict.


  • Organizational Affiliation

    CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LAN-DAP5 DERIVATIVE OF LANREOTIDE
A, B
9Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DNP
Query on DNP
A, B
L-PEPTIDE LINKINGC3 H9 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.83 Å
  • R-Value Free: 0.086 
  • R-Value Work: 0.077 
  • R-Value Observed: 0.078 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 18.95α = 90
b = 18.95β = 90
c = 57.52γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection
  • Version 1.2: 2023-10-18
    Changes: Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection