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- PDB-9btq: Cryo-EM structure of extracellular tube from Microcystis Aerugino... -

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Basic information

Entry
Database: PDB / ID: 9btq
TitleCryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Componentspilin
KeywordsPROTEIN FIBRIL / extracellular tube / filament / pili / helical symmetry
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMicrocystis aeruginosa PCC 7806SL (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsPetersen, H.A. / Ricca, J.G. / Louda, J.W. / Wang, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of extracellular tube from Microcystis Aeruginosa pcc 7806SL
Authors: Petersen, H.A. / Ricca, J.G. / Louda, J.W. / Wang, F.
History
DepositionMay 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data 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: pilin


Theoretical massNumber of molelcules
Total (without water)15,5151
Polymers15,5151
Non-polymers00
Water00
1
A: pilin
x 40


Theoretical massNumber of molelcules
Total (without water)620,61140
Polymers620,61140
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation39
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 40 / Rise per n subunits: 3.648 Å / Rotation per n subunits: -14.737 °)

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Components

#1: Protein pilin


Mass: 15515.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Microcystis aeruginosa PCC 7806SL (bacteria)
References: UniProt: L7EE41
Has ligand of interestN
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: pili filaments / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Microcystis aeruginosa PCC 7806SL (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -14.74 ° / Axial rise/subunit: 3.69 Å / Axial symmetry: C1
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1875465 / Symmetry type: HELICAL
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00640440
ELECTRON MICROSCOPYf_angle_d1.12855440
ELECTRON MICROSCOPYf_dihedral_angle_d5.0565160
ELECTRON MICROSCOPYf_chiral_restr0.0587960
ELECTRON MICROSCOPYf_plane_restr0.0046480

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