13MF | pdb_000013mf

4-fluoro-L-phenylalanine bolaphile peptide

PDB DOI: https://doi.org/10.2210/pdb13MF/pdb
EM Map EMD-77153: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2026-05-13 Released: 2026-09-23
Deposition Author(s): Das, A., Conticello, V.P., Wang, F., Zia, A., Eastep, G.N.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Chemical Editing Reveals Atomic-Level Control of Supramolecular Structure in Self-Assembling Peptides.

Das, A., Zia, A., Eastep, G.N., Wang, F., Conticello, V.P.

(2026) J Am Chem Soc 148: 40186-40197

PubMed: 42938080 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.6c11510
Primary Citation Related Structures:
13FM, 13MF

PubMed Abstract:
Can replacement of single atoms within amino acid sequences redirect peptide self-assembly into different supramolecular structures? To address this question, we investigated a compositionally similar class of bola-amphiphilic peptides that were designed to self-assemble into filamentous nanostructures. The chemical differences between these peptides were confined to minimally perturbative substitutions on a phenylalanine side chain at a single site within the sequence. Cryo-EM structural analysis of five peptide filaments at near-atomic resolution revealed the presence of distinct supramolecular architectures between the different peptides. Despite sharing a common cross-β framework, the filament structures displayed distinct helical symmetries, protofilament organizations, and steric zipper interfaces. We hypothesize that the observed structural divergence between filaments arises from subtle changes in side-chain polarity and solvent interactions that remodel peptide packing at structural interfaces within cross-sectional amyloid layers. These findings demonstrate that the supramolecular structural landscape of self-assembling peptides is sensitive to atomic-level substitution and suggest that chemical editing provides a strategy for interrogating and potentially controlling biomolecular assembly. These results further highlight a fundamental limitation in the predictive design of peptide-based materials in that subtle chemical modifications in local composition can produce disproportionate changes in higher-order structure.

Organizational Affiliation

Department of Chemistry, Emory University, Atlanta, Georgia30322, United States.

Macromolecule Content

Total Structure Weight: 56.35 kDa
Atom Count: 4,060
Modeled Residue Count: 560
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-LYS-ILE-ILE-ILE-PFF-LYS-NH2	A [auth 0] AA [auth AR] AB [auth i] B [auth 1] BA [auth AS] A [auth 0], AA [auth AR], AB [auth i], B [auth 1], BA [auth AS], BB [auth j], C [auth 2], CA [auth AT], CB [auth k], D [auth 3], DA [auth K], DB [auth l], E [auth 4], EA [auth L], EB [auth m], F [auth 5], FA [auth M], FB [auth n], G [auth 6], GA [auth N], GB [auth o], H [auth 7], HA [auth O], HB [auth p], I [auth 8], IA [auth P], IB [auth q], J [auth 9], JA [auth Q], JB [auth r], K [auth AA], KA [auth R], KB [auth s], L [auth AB], LA [auth S], LB [auth t], M [auth AC], MA [auth T], MB [auth u], N [auth AD], NA [auth U], NB [auth v], O [auth AE], OA [auth W], OB [auth w], P [auth AF], PA [auth X], PB [auth x], Q [auth AG], QA [auth Y], QB [auth y], R [auth AH], RA [auth Z], RB [auth z], S [auth AI], SA [auth a], T [auth AJ], TA [auth b], U [auth AK], UA [auth c], V [auth AM], VA [auth d], W [auth AN], WA [auth e], X [auth AO], XA [auth f], Y [auth AP], YA [auth g], Z [auth AQ], ZA [auth h]	8	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
PFF Query on PFF	A [auth 0], AA [auth AR], AB [auth i], B [auth 1], BA [auth AS] A [auth 0], AA [auth AR], AB [auth i], B [auth 1], BA [auth AS], BB [auth j], C [auth 2], CA [auth AT], CB [auth k], D [auth 3], DA [auth K], DB [auth l], E [auth 4], EA [auth L], EB [auth m], F [auth 5], FA [auth M], FB [auth n], G [auth 6], GA [auth N], GB [auth o], H [auth 7], HA [auth O], HB [auth p], I [auth 8], IA [auth P], IB [auth q], J [auth 9], JA [auth Q], JB [auth r], K [auth AA], KA [auth R], KB [auth s], L [auth AB], LA [auth S], LB [auth t], M [auth AC], MA [auth T], MB [auth u], N [auth AD], NA [auth U], NB [auth v], O [auth AE], OA [auth W], OB [auth w], P [auth AF], PA [auth X], PB [auth x], Q [auth AG], QA [auth Y], QB [auth y], R [auth AH], RA [auth Z], RB [auth z], S [auth AI], SA [auth a], T [auth AJ], TA [auth b], U [auth AK], UA [auth c], V [auth AM], VA [auth d], W [auth AN], WA [auth e], X [auth AO], XA [auth f], Y [auth AP], YA [auth g], Z [auth AQ], ZA [auth h]	PHE	Fluorination	C₉ H₁₀ F N O₂