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- PDB-9bjn: Cryo-EM of Azo-ffspy fiber -

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Basic information

Entry
Database: PDB / ID: 9bjn
TitleCryo-EM of Azo-ffspy fiber
ComponentsD-peptide ffspy
KeywordsPROTEIN FIBRIL / D-peptide / peptide-fiber / helical
Function / homologypolypeptide(D)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsZia, A. / Guo, J. / Xu, B. / Wang, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
CitationJournal: J Am Chem Soc / Year: 2024
Title: Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars.
Authors: Jiaqi Guo / Ayisha Zia / Qianfeng Qiu / Michael Norton / Kangqiang Qiu / Junichi Usuba / Zhiyu Liu / Meihui Yi / Shane T Rich-New / Michael Hagan / Seth Fraden / Grace D Han / Jiajie Diao / ...Authors: Jiaqi Guo / Ayisha Zia / Qianfeng Qiu / Michael Norton / Kangqiang Qiu / Junichi Usuba / Zhiyu Liu / Meihui Yi / Shane T Rich-New / Michael Hagan / Seth Fraden / Grace D Han / Jiajie Diao / Fengbin Wang / Bing Xu /
Abstract: Cells contain intricate protein nanostructures, but replicating them outside of cells presents challenges. One such example is the vertical fibronectin pillars observed in embryos. Here, we ...Cells contain intricate protein nanostructures, but replicating them outside of cells presents challenges. One such example is the vertical fibronectin pillars observed in embryos. Here, we demonstrate the creation of cell-free vertical fibronectin pillar mimics using nonequilibrium self-assembly. Our approach utilizes enzyme-responsive phosphopeptides that assemble into nanotubes. Enzyme action triggers shape changes in peptide assemblies, driving the vertical growth of protein nanopillars into bundles. These bundles, with peptide nanotubes serving as a template to remodel fibronectin, can then recruit collagen, which forms aggregates or bundles depending on their types. Nanopillar formation relies on enzyme-catalyzed nonequilibrium self-assembly and is governed by the concentrations of enzyme, protein, peptide, the structure of the peptide, and peptide assembly morphologies. Cryo-EM reveals unexpected nanotube thinning and packing after dephosphorylation, indicating a complex sculpting process during assembly. Our study demonstrates a cell-free method for constructing intricate, multiprotein nanostructures with directionality and composition.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Data collection / Database references / Derived calculations
Category: citation / em_admin / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-peptide ffspy


Theoretical massNumber of molelcules
Total (without water)8511
Polymers8511
Non-polymers00
Water00
1
A: D-peptide ffspy
x 24


  • representative helical assembly
  • Evidence: electron microscopy, not applicable
  • 20.4 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)20,41924
Polymers20,41924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation23
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 2 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 24 / Rise per n subunits: 1.162 Å / Rotation per n subunits: 46.52 °)

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Components

#1: Polypeptide(D) D-peptide ffspy


Mass: 850.809 Da / Num. of mol.: 1 / 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: ffspy fiber / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
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: 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 46.52 ° / Axial rise/subunit: 1.162 Å / Axial symmetry: C2
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 887952 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0095040
ELECTRON MICROSCOPYf_angle_d2.6346640
ELECTRON MICROSCOPYf_dihedral_angle_d18.9831040
ELECTRON MICROSCOPYf_chiral_restr0.041320
ELECTRON MICROSCOPYf_plane_restr0.011640

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