[English] 日本語
Yorodumi
- PDB-9s7q: Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s7q
TitleCryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 2 in PBS pH 6.5
ComponentsBrevinin-1OKc
KeywordsANTIMICROBIAL PROTEIN / Amyloid / Antimicrobial
Function / homologykilling of cells of another organism / defense response to Gram-positive bacterium / AbyA5
Function and homology information
Biological speciesNidirana okinavana (Kampira Falls frog)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsRagonis-Bachar, P. / Strati, F. / Gustavsson, E. / Khokhlov, A. / Barnea, E. / Rayan, B. / Upchr, A. / Landau, M.
Funding supportEuropean Union, Israel, Germany, 8items
OrganizationGrant numberCountry
European Research Council (ERC)101087140European Union
Israel Science Foundation2111/20 Israel
Volkswagen Foundation76251-4659/2022 (ZN 4042) Germany
German Research Foundation (DFG)152/772-1 Germany
German Research Foundation (DFG)152/774-1 Germany
German Research Foundation (DFG)152/775-1 Germany
German Research Foundation (DFG)152/776-1 Germany
German Research Foundation (DFG)152/777-1 FUGG Germany
CitationJournal: To Be Published
Title: Amyloidogenic Nature and Structural Polymorphism of Antimicrobial, Virulent and Defense Peptides
Authors: Ragonis-Bachar, P. / Strati, F. / Gustavsson, E. / Khokhlov, A. / Barnea, E. / Rayan, B. / Upchr, A. / Landau, M.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 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
A: Brevinin-1OKc
B: Brevinin-1OKc
C: Brevinin-1OKc
D: Brevinin-1OKc
E: Brevinin-1OKc
F: Brevinin-1OKc
G: Brevinin-1OKc
H: Brevinin-1OKc
I: Brevinin-1OKc
J: Brevinin-1OKc
K: Brevinin-1OKc
L: Brevinin-1OKc
M: Brevinin-1OKc
N: Brevinin-1OKc
O: Brevinin-1OKc
P: Brevinin-1OKc
Q: Brevinin-1OKc
R: Brevinin-1OKc


Theoretical massNumber of molelcules
Total (without water)40,94718
Polymers40,94718
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
Brevinin-1OKc


Mass: 2274.832 Da / Num. of mol.: 18 / Source method: obtained synthetically / Source: (synth.) Nidirana okinavana (Kampira Falls frog) / References: UniProt: C0HL10
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Brevinin-1OKc / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Nidirana okinavana (Kampira Falls frog)
Buffer solutionpH: 6.5 / Details: 1xPBS pH 6.5 from Sigma Aldrich
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was fibrillated in PBS pH 6.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 298 K

-
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: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.92model fitting
9Servalcatmodel refinement
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 59.5 ° / Axial rise/subunit: 1.6 Å / Axial symmetry: C2
Particle selectionNum. of particles selected: 328282
3D reconstructionResolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312286 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingDetails: De novo generated in Coot / Source name: Other / Type: other

+
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