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- EMDB-13830: Lanreotide nanotube -

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Basic information

Entry
Database: EMDB / ID: EMD-13830
TitleLanreotide nanotube
Map data
Sample
  • Complex: Lanreotide
    • Protein or peptide: Lanreotide
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsPieri L / Wang F / Arteni AA / Bressanelli S / Egelman EH / Paternostre M
Funding support France, United States, 3 items
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, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 6, 2022-
Current statusApr 6, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13830.png

Downloads & links

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Map

FileDownload / File: emd_13830.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1102 Å
Density
Contour LevelBy AUTHOR: 0.362
Minimum - Maximum-1.02016 - 1.7793083
Average (Standard dev.)0.005300911 (±0.085088626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Lanreotide

EntireName: Lanreotide
Components
  • Complex: Lanreotide
    • Protein or peptide: Lanreotide

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Supramolecule #1: Lanreotide

SupramoleculeName: Lanreotide / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.096 kDa/nm

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Macromolecule #1: Lanreotide

MacromoleculeName: Lanreotide / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.098339 KDa
SequenceString:
(4J2)CY(DTR)KVCT(NH2)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration20 mg/mL
BufferpH: 6 / Component - Concentration: 40.0 mg/ml / Component - Name: Pure water
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.039 kPa / Details: Current intensity 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 30 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: No corrector / Chromatic aberration corrector: No corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Bioquantum + K3 camera
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 19497 / Average exposure time: 1.69 sec. / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 20
Applied symmetry - Helical parameters - Δz: 1.04 Å
Applied symmetry - Helical parameters - Δ&Phi: 26.219 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 2264921
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2)
Segment selectionNumber selected: 5109922 / Software - Name: cryoSPARC (ver. 3.2) / Details: Template-based picking
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7q5a:
Lanreotide nanotube

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