[English] 日本語
Yorodumi
- PDB-13fm: 3,5-difluoro-L-phenylalanine bolaphile peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 13fm
Title3,5-difluoro-L-phenylalanine bolaphile peptide
ComponentsACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
KeywordsPROTEIN FIBRIL / Peptide nanotube / Amphiphile / Amyloids / helical
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDas, A. / Conticello, V.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Chemical Editing Reveals Atomic-Level Control of Supramolecular Structure in Self-Assembling Peptides
Authors: Das, A. / Zia, A. / Eastep, G.N. / Wang, F. / Conticello, V.P.
History
DepositionMay 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Y: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
f: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
e: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
d: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
c: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
b: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
a: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
Z: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
g: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
n: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
m: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
l: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
k: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
j: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
i: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
h: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
o: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
v: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
u: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
t: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
s: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
r: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
q: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
p: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
w: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
4: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
3: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
2: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
1: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
z: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
y: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
x: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
5: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AB: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AA: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
0: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
9: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
8: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
7: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
6: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AC: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AJ: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AI: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AH: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AG: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AF: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AE: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AD: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AK: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AR: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AQ: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AP: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AO: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AN: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AM: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AL: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AS: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AZ: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AY: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AX: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AW: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AV: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AU: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
AT: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2


Theoretical massNumber of molelcules
Total (without water)52,67564
Polymers52,67564
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein/peptide ...
ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2


Mass: 823.049 Da / Num. of mol.: 64 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Synthetic amyloid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.19 ° / Axial rise/subunit: 2.45506 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7069 / Symmetry type: HELICAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more