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- PDB-9egp: Cryo-EM of type IV pilus from Geobacter metallireducens -

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Basic information

Entry
Database: PDB / ID: 9egp
TitleCryo-EM of type IV pilus from Geobacter metallireducens
Components
  • Geopilin domain 1 protein
  • Geopilin domain 2 protein
KeywordsPROTEIN FIBRIL / pilus / type iv pilus / helical symmetry
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Geopilin domain 2 protein / Geopilin domain 1 protein
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsEgorova, M. / Petersen, H.A. / Chan, C.H. / Bond, D.R. / 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 of type IV pilus from Geobacter metallireducens
Authors: Egorova, M. / Petersen, H.A. / Chan, C.H. / Bond, D.R. / Wang, F.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 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
B: Geopilin domain 2 protein
A: Geopilin domain 1 protein


Theoretical massNumber of molelcules
Total (without water)19,4362
Polymers19,4362
Non-polymers00
Water00
1
B: Geopilin domain 2 protein
A: Geopilin domain 1 protein
x 24


Theoretical massNumber of molelcules
Total (without water)466,46448
Polymers466,46448
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation23
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: 24 / Rise per n subunits: 10.094 Å / Rotation per n subunits: 91.753 °)

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Components

#1: Protein Geopilin domain 2 protein


Mass: 11607.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacter metallireducens (bacteria) / References: UniProt: Q39VU0
#2: Protein Geopilin domain 1 protein


Mass: 7828.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacter metallireducens (bacteria) / References: UniProt: Q39VU1
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: type IV pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Geobacter metallireducens (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: 91.753 ° / Axial rise/subunit: 10.094 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193496 / Symmetry type: HELICAL
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327552
ELECTRON MICROSCOPYf_angle_d0.58637536
ELECTRON MICROSCOPYf_dihedral_angle_d6.0833864
ELECTRON MICROSCOPYf_chiral_restr0.0394416
ELECTRON MICROSCOPYf_plane_restr0.0034800

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