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- PDB-8gi5: Cryo-EM of self-assembling pyrene peptide with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 8gi5
TitleCryo-EM of self-assembling pyrene peptide with Ca2+
ComponentsPyrene peptide
KeywordsPROTEIN FIBRIL / peptides / nanofibers / self-assembly peptide filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsRich-New, S.T. / Guo, J. / Xu, B. / Wang, F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: Chem / Year: 2023
Title: Hierarchical Assembly of Intrinsically Disordered Short Peptides.
Authors: Jiaqi Guo / Shane T Rich-New / Chen Liu / Yimeng Huang / Weiyi Tan / Hongjian He / Meihui Yi / Xixiang Zhang / Edward H Egelman / Fengbin Wang / Bing Xu /
Abstract: The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short ...The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.
History
DepositionMar 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrene peptide
B: Pyrene peptide
C: Pyrene peptide
D: Pyrene peptide


Theoretical massNumber of molelcules
Total (without water)4,2404
Polymers4,2404
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Pyrene peptide


Mass: 1060.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pyrene peptide with Ca2+ / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.8 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C2
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1380792 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023344
ELECTRON MICROSCOPYf_angle_d0.7644768
ELECTRON MICROSCOPYf_dihedral_angle_d51.643416
ELECTRON MICROSCOPYf_chiral_restr0.031272
ELECTRON MICROSCOPYf_plane_restr0.01400

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