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- PDB-9mfu: Cryo-EM of helical fibers formed by (NAP)FFGPQYQP -

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Basic information

Entry
Database: PDB / ID: 9mfu
TitleCryo-EM of helical fibers formed by (NAP)FFGPQYQP
Components(I7L)FFGPQYQP
KeywordsPROTEIN FIBRIL / peptide fiber / helical polymer
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZia, A. / Qiao, Y. / 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: Angew Chem Int Ed Engl / Year: 2025
Title: Intrinsically Disordered Peptide Nanofibers from a Structured Motif Within Proteins.
Authors: Yuchen Qiao / Ayisha Zia / Adrianna Shy / Grace Wu / Matthew Chu / Zhiyu Liu / Fengbin Wang / Bing Xu /
Abstract: Intrinsically disordered regions (IDRs) are ubiquitous in proteins, orchestrating complex cellular signaling through higher-order protein assemblies. However, the properties and functions of ...Intrinsically disordered regions (IDRs) are ubiquitous in proteins, orchestrating complex cellular signaling through higher-order protein assemblies. However, the properties and functions of intrinsically disordered peptide (IDP) assemblies are largely underexplored. This work unveiled a facile strategy for engineering IDP assemblies. We demonstrate that conjugating a structured motif derived from a protein's phosphorylation site to a self-assembling tripeptide unexpectedly yields self-assembled nanofibers with intrinsic disorder. Specifically, by using a glycine linker to attach a pentapeptide derived from a phosphorylation site within a random coil region of SRC kinase to the C-terminus of a widely used self-assembling enabler, we generated a phosphorylated octapeptide. The octapeptide exhibits cell compatibility and forms a hydrogel upon dephosphorylation of the phosphooctapeptide. Cryo-electron microscopy (cryo-EM) structural analysis of the nanofibers reveals that the peptides adopt two types of helical arrangements but exhibit intrinsic disorder at the periphery of the nanofibers. The hydrogels exhibit decreased protein adsorption with increasing peptide concentration. This study represents the first instance of a structured random coil within a protein transitioning into an intrinsically disordered state within self-assembled peptide nanofibers, expanding the pool of peptide sequences for IDPs and providing valuable insights for the engineering of peptide nanofibers with intrinsic disorder for the development of cell-compatible biomaterials.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (I7L)FFGPQYQP
B: (I7L)FFGPQYQP
D: (I7L)FFGPQYQP
E: (I7L)FFGPQYQP
F: (I7L)FFGPQYQP
G: (I7L)FFGPQYQP
X: (I7L)FFGPQYQP


Theoretical massNumber of molelcules
Total (without water)8,0597
Polymers8,0597
Non-polymers00
Water00
1
A: (I7L)FFGPQYQP
B: (I7L)FFGPQYQP
D: (I7L)FFGPQYQP
E: (I7L)FFGPQYQP
F: (I7L)FFGPQYQP
G: (I7L)FFGPQYQP
X: (I7L)FFGPQYQP
x 14


Theoretical massNumber of molelcules
Total (without water)112,82498
Polymers112,82498
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation13
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: 7 / Rise per n subunits: 5.04 Å / Rotation per n subunits: -2.55 °)

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Components

#1: Protein/peptide
(I7L)FFGPQYQP


Mass: 1151.267 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
Has protein modificationY

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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: (I7L)FFGPQYQP / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
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: TFS 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

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.55 ° / Axial rise/subunit: 5.04 Å / Axial symmetry: C2
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 858964 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034088
ELECTRON MICROSCOPYf_angle_d0.7345408
ELECTRON MICROSCOPYf_dihedral_angle_d14.524456
ELECTRON MICROSCOPYf_chiral_restr0.028296
ELECTRON MICROSCOPYf_plane_restr0.01648

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