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- EMDB-55504: Nonameric Ena1C ring of Bacillus cereus -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-55504
TitleNonameric Ena1C ring of Bacillus cereus
Map data
Sample
  • Complex: Ena1C
    • Protein or peptide: DUF3992 domain-containing protein
KeywordsS-ENA / ENA anchoring / spore coat anchoring / endospore / PROTEIN FIBRIL
Function / homologyEndospore appendages core / Endospore appendages / DUF3992 domain-containing protein
Function and homology information
Biological speciesBacillus paranthracis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionOct 28, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55504.png

Downloads & links

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Map

FileDownload / File: emd_55504.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 104 pix.
= 144.56 Å		1.39 Å/pix.
x 104 pix.
= 144.56 Å		1.39 Å/pix.
x 104 pix.
= 144.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.148
Minimum - Maximum-0.16915427 - 0.45233667
Average (Standard dev.)0.003908444 (±0.032975566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions104104104
Spacing104104104
CellA=B=C: 144.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55504_msk_1.map
Projections & Slices
AxesZYX

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Additional map: B-factor sharpened with solvent mask

Fileemd_55504_additional_1.map
AnnotationB-factor sharpened with solvent mask
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Additional map: EMready postprocessed

Fileemd_55504_additional_2.map
AnnotationEMready postprocessed
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_55504_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55504_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : Ena1C

EntireName: Ena1C
Components
  • Complex: Ena1C
    • Protein or peptide: DUF3992 domain-containing protein

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Supramolecule #1: Ena1C

SupramoleculeName: Ena1C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus paranthracis (bacteria)

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Macromolecule #1: DUF3992 domain-containing protein

MacromoleculeName: DUF3992 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bacillus paranthracis (bacteria)
Molecular weightTheoretical: 18.929354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHSSG ENLYFQGKPH KNIGCFAPLS IICQPTCPCP PPILPPERGD AELVTNEFAG DILISNDFIP ISQKQLKQTN TTVNIWKND GIVSLSGTIS IYNNRNSTNA LSIQIISSTT NTFTALPGNT ISYTGFDLQS VSVIDIPSDP SIYIEGRYCF Q LTYCKSKR DCL

UniProtKB: DUF3992 domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 412005
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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