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- PDB-7q5a: Lanreotide nanotube -

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Basic information

Entry
Database: PDB / ID: 7q5a
TitleLanreotide nanotube
ComponentsLanreotide
KeywordsHORMONE / Lanreotide / nanotube / assembly
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsPieri, L. / Wang, F. / Arteni, A.A. / Bressanelli, S. / Egelman, E.H. / Paternostre, M.
Funding support France, United States, 3items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Atomic structure of Lanreotide nanotubes revealed by cryo-EM.
Authors: Laura Pieri / Fengbin Wang / Ana-Andreea Arteni / Matthijn Vos / Jean-Marie Winter / Marie-Hélène Le Du / Franck Artzner / Frédéric Gobeaux / Pierre Legrand / Yves Boulard / Stéphane ...Authors: Laura Pieri / Fengbin Wang / Ana-Andreea Arteni / Matthijn Vos / Jean-Marie Winter / Marie-Hélène Le Du / Franck Artzner / Frédéric Gobeaux / Pierre Legrand / Yves Boulard / Stéphane Bressanelli / Edward H Egelman / Maité Paternostre /
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 ...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.
History
DepositionNov 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanreotide
B: Lanreotide
C: Lanreotide
D: Lanreotide
E: Lanreotide
F: Lanreotide
G: Lanreotide
H: Lanreotide


Theoretical massNumber of molelcules
Total (without water)8,7878
Polymers8,7878
Non-polymers00
Water00
1
A: Lanreotide
B: Lanreotide
C: Lanreotide
D: Lanreotide
E: Lanreotide
F: Lanreotide
G: Lanreotide
H: Lanreotide
x 100


Theoretical massNumber of molelcules
Total (without water)878,671800
Polymers878,671800
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation99

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Components

#1: Protein/peptide
Lanreotide


Mass: 1098.339 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Lanreotide / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 1.096 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 6
Buffer componentConc.: 40 mg/ml / Name: Pure water
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Current intensity 15 mA / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: Blot for 30 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.69 sec. / Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 19497
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: No corrector / Details: Bioquantum + K3 camera / Energyfilter slit width: 20 eV / Spherical aberration corrector: No corrector
Image scansWidth: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2particle selection
2EPU2.12.1.278RELimage acquisitionFEI Thermofisher
4cryoSPARC3.2CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARC3.2initial Euler assignment
11cryoSPARC3.2final Euler assignment
12cryoSPARC3.2classification
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 26.219 ° / Axial rise/subunit: 1.04 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 5109922 / Details: Template-based picking
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2264921 / Num. of class averages: 20 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 18.52 Å2

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