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- PDB-9vp4: CryoEM structure of cyclised H-pilus (D69R) -

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Basic information

Entry
Database: PDB / ID: 9vp4
TitleCryoEM structure of cyclised H-pilus (D69R)
ComponentsPilin
KeywordsPROTEIN FIBRIL / pilus / conjugation / filament
Function / homology1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Pilin
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsIshimoto, N. / Beis, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Surface electrostatic potential affects mating pilus functionality
Authors: He, S. / Ishimoto, N. / Wong, J. / David, S. / Beis, K. / Frankel, G.
History
DepositionJul 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3672
Polymers7,6441
Non-polymers7231
Water00
1
A: Pilin
hetero molecules
x 104


Theoretical massNumber of molelcules
Total (without water)870,170208
Polymers794,981104
Non-polymers75,189104
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation103

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Components

#1: Protein Pilin


Mass: 7644.048 Da / Num. of mol.: 1 / Mutation: D69R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: trhA, HCM1.67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q935P5
#2: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: H-Pilus (D69R) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.1 kDa/nm / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIX1.20.1_4487model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 29 ° / Axial rise/subunit: 12.26 Å / Axial symmetry: C5
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 695564 / Num. of class averages: 1 / Symmetry type: HELICAL
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002558
ELECTRON MICROSCOPYf_angle_d0.364741
ELECTRON MICROSCOPYf_dihedral_angle_d11.49106
ELECTRON MICROSCOPYf_chiral_restr0.03381
ELECTRON MICROSCOPYf_plane_restr0.00585

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