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- PDB-7uuq: Cryo-EM of self-assembling pyrene IDP -

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Basic information

Entry
Database: PDB / ID: 7uuq
TitleCryo-EM of self-assembling pyrene IDP
ComponentsPyrene-containing peptide fibril
KeywordsPROTEIN FIBRIL / peptides / nanofibers / self-assembly peptide filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang, F. / Guo, J. / Xu, B. / Egelman, E.H.
Funding support United States, 4items
OrganizationGrant numberCountry
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
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
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_struct_assembly
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_assembly.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrene-containing peptide fibril
B: Pyrene-containing peptide fibril
C: Pyrene-containing peptide fibril
D: Pyrene-containing peptide fibril
E: Pyrene-containing peptide fibril
F: Pyrene-containing peptide fibril
G: Pyrene-containing peptide fibril


Theoretical massNumber of molelcules
Total (without water)7,4207
Polymers7,4207
Non-polymers00
Water00
1
A: Pyrene-containing peptide fibril
B: Pyrene-containing peptide fibril
C: Pyrene-containing peptide fibril
D: Pyrene-containing peptide fibril
E: Pyrene-containing peptide fibril
F: Pyrene-containing peptide fibril
G: Pyrene-containing peptide fibril
x 14


Theoretical massNumber of molelcules
Total (without water)103,88198
Polymers103,88198
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation13
MethodUCSF CHIMERA

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Components

#1: Protein/peptide
Pyrene-containing peptide fibril


Mass: 1060.007 Da / Num. of mol.: 7 / 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 IDR / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 3000 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: -5.38 ° / Axial rise/subunit: 4.74 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 461253 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.015222
ELECTRON MICROSCOPYf_angle_d1.5777420
ELECTRON MICROSCOPYf_dihedral_angle_d39.6911260
ELECTRON MICROSCOPYf_chiral_restr0.058420
ELECTRON MICROSCOPYf_plane_restr0.011630

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