[English] 日本語
Yorodumi
- EMDB-52151: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52151
TitleAmyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
Map data
Sample
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
    • Protein or peptide: Citropin-1.3
KeywordsAmyloid Helical / ANTIMICROBIAL PROTEIN
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Citropin-1.3
Function and homology information
Biological speciesRanoidea citropa (Blue Mountains treefrog)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsStrati F / Rayan B / Pigozzi CM / Bloch Y / Mostafavi S / Monistrol J / Golubev A / Gustavsson E / Landau M
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101087140European Union
Other private
CitationJournal: To Be Published
Title: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
Authors: Strati F / Pigozzi CM / Bloch Y / Mostafavi S / Monistrol J / Golubev A / Gustavsson E / Landau M
History
DepositionNov 19, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52151.png

Downloads & links

-
Map

FileDownload / File: emd_52151.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 250 pix.
= 212.5 Å		0.85 Å/pix.
x 250 pix.
= 212.5 Å		0.85 Å/pix.
x 250 pix.
= 212.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.013302121 - 0.025769228
Average (Standard dev.)0.000086181666 (±0.0013197425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 212.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52151_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52151_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52151_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly...

EntireName: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
Components
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
    • Protein or peptide: Citropin-1.3

-
Supramolecule #1: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly...

SupramoleculeName: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)
Molecular weightTheoretical: 0.16 kDa/nm

-
Macromolecule #1: Citropin-1.3

MacromoleculeName: Citropin-1.3 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)
Molecular weightTheoretical: 1.631998 KDa
SequenceString:
GLFDIIKKVA SVIGGL

UniProtKB: Citropin-1.3

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.86 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.83 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126916
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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