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- PDB-7q5g: LAN-DAP5 DERIVATIVE OF LANREOTIDE: L-DIAMINO PROPIONIC ACID IN PO... -

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Basic information

Entry
Database: PDB / ID: 7q5g
TitleLAN-DAP5 DERIVATIVE OF LANREOTIDE: L-DIAMINO PROPIONIC ACID IN POSITION 5 IN PLACE OF L-LYSINE
ComponentsLAN-DAP5 DERIVATIVE OF LANREOTIDE
KeywordsHORMONE / Lanreotide / nanotube / assembly
Function / homologyETHANOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.83 Å
AuthorsBressanelli, S. / Le Du, M.H. / Gobeaux, F. / Legrand, P. / Paternostre, M.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
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 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Oct 18, 2023Group: Data collection / Category: emd_author_list
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAN-DAP5 DERIVATIVE OF LANREOTIDE
B: LAN-DAP5 DERIVATIVE OF LANREOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2054
Polymers2,1132
Non-polymers922
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Lanreotide determined to dimerize rpior to self-assembly. Uncertain about Lan-dap5
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint1 kcal/mol
Surface area2200 Å2
Unit cell
Length a, b, c (Å)18.950, 18.950, 57.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein/peptide LAN-DAP5 DERIVATIVE OF LANREOTIDE


Mass: 1056.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.41 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ethanol 29%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.79990, 0.78971
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.79991
20.789711
ReflectionResolution: 0.825→16.41 Å / Num. obs: 11135 / % possible obs: 99.18 % / Redundancy: 44.4 % / Biso Wilson estimate: 4.77 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.02957 / Rpim(I) all: 0.004005 / Rrim(I) all: 0.02985 / Net I/σ(I): 90.68
Reflection shellResolution: 0.825→0.8546 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.1596 / Mean I/σ(I) obs: 7.14 / Num. unique obs: 1011 / CC1/2: 0.975 / CC star: 0.994 / Rpim(I) all: 0.07567 / Rrim(I) all: 0.1784 / % possible all: 91.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.83→16.41 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 8.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.0858 1113 10 %
Rwork0.0773 10019 -
obs0.0781 11132 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 19.59 Å2 / Biso mean: 5.8883 Å2 / Biso min: 3.11 Å2
Refinement stepCycle: final / Resolution: 0.83→16.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms148 0 24 8 180
Biso mean--10.01 10.53 -
Num. residues----16
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.83-0.860.13111280.11311182131094
0.86-0.910.09541400.086712621402100
0.91-0.960.11410.079312481389100
0.97-1.040.08221380.067712531391100
1.04-1.140.06571390.06312721411100
1.14-1.310.08361400.069912571397100
1.31-1.650.08181460.075412671413100
1.65-16.410.08641410.081312781419100

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