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- PDB-9ihh: Ex vivo spore-silk A-ENA fibers -

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Basic information

Entry
Database: PDB / ID: 9ihh
TitleEx vivo spore-silk A-ENA fibers
ComponentsEx vivo spore-silk A-ENA fibers
KeywordsPROTEIN FIBRIL / endospore / isopeptide bond / A-ENA / cross-linked / protein fiber / autocatalytic
Function / homology: / Alpha-helical endospore appendage domain / Uncharacterized protein
Function and homology information
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSleutel, M. / Sogues, A. / Remaut, H.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
Citation
Journal: To Be Published
Title: Auto-crosslinking sporesilk fibers promote endospore clustering and Cry toxin retention in Bacillus thuringiensis
Authors: Sleutel, M. / Sogues, A. / Remaut, H.
#1: Journal: 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
DepositionFeb 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ex vivo spore-silk A-ENA fibers
B: Ex vivo spore-silk A-ENA fibers
C: Ex vivo spore-silk A-ENA fibers
D: Ex vivo spore-silk A-ENA fibers
E: Ex vivo spore-silk A-ENA fibers
F: Ex vivo spore-silk A-ENA fibers
G: Ex vivo spore-silk A-ENA fibers
H: Ex vivo spore-silk A-ENA fibers
I: Ex vivo spore-silk A-ENA fibers
J: Ex vivo spore-silk A-ENA fibers
K: Ex vivo spore-silk A-ENA fibers
L: Ex vivo spore-silk A-ENA fibers
M: Ex vivo spore-silk A-ENA fibers
N: Ex vivo spore-silk A-ENA fibers
O: Ex vivo spore-silk A-ENA fibers
a: Ex vivo spore-silk A-ENA fibers
b: Ex vivo spore-silk A-ENA fibers
c: Ex vivo spore-silk A-ENA fibers
d: Ex vivo spore-silk A-ENA fibers
e: Ex vivo spore-silk A-ENA fibers
f: Ex vivo spore-silk A-ENA fibers
g: Ex vivo spore-silk A-ENA fibers
h: Ex vivo spore-silk A-ENA fibers
i: Ex vivo spore-silk A-ENA fibers
j: Ex vivo spore-silk A-ENA fibers
k: Ex vivo spore-silk A-ENA fibers
l: Ex vivo spore-silk A-ENA fibers
m: Ex vivo spore-silk A-ENA fibers
n: Ex vivo spore-silk A-ENA fibers


Theoretical massNumber of molelcules
Total (without water)316,60929
Polymers316,60929
Non-polymers00
Water10,791599
1


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

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Components

#1: Protein ...
Ex vivo spore-silk A-ENA fibers


Mass: 10917.550 Da / Num. of mol.: 29
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis (bacteria)
Gene: ATN07_33990, BTAR23_AR23_06116
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
References: UniProt: Q8KNV8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Ex vivo spore-silk A-ENA fibers / Type: CELL / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Bacillus thuringiensis serovar israelensis (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 3000 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -173.6 ° / Axial rise/subunit: 5.37 Å / Axial symmetry: C1
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 532909 / Symmetry type: HELICAL

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