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- PDB-9hvc: CryoEM structure of cyclised H-pilus -

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Basic information

Entry
Database: PDB / ID: 9hvc
TitleCryoEM structure of cyclised H-pilus
ComponentsPili assembly chaperone
KeywordsPROTEIN FIBRIL / Pilus / Conjugation / Filament
Function / homologymembrane / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Pili assembly chaperone
Function and homology information
Biological speciesSalmonella (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsIshimoto, N. / Beis, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cryoEM structure of H-pilus
Authors: Ishimoto, N. / Beis, K.
History
DepositionDec 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 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
A: Pili assembly chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3252
Polymers7,6021
Non-polymers7231
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Helical Rise and Twist, mass spectrometry, Cyclisation between N and C terminus.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Pili assembly chaperone


Mass: 7601.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last five residues of AGIPL are cleaved when H-pilus make cyclisation.
Source: (gene. exp.) Salmonella (bacteria) / Gene: GDL44_23070 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6W0B860
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.1 kDa/nm / Experimental value: YES
Source (natural)Organism: Salmonella (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: 1800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 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
7Buccaneermodel fitting
8UCSF ChimeraXmodel fitting
9Cootmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
15PHENIX1.20.1_4487model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 28.93 ° / Axial rise/subunit: 12.14 Å / Axial symmetry: C5
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123942 / Num. of class averages: 1 / Symmetry type: HELICAL
RefinementHighest resolution: 2.24 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003555
ELECTRON MICROSCOPYf_angle_d0.366738
ELECTRON MICROSCOPYf_dihedral_angle_d14.487105
ELECTRON MICROSCOPYf_chiral_restr0.03581
ELECTRON MICROSCOPYf_plane_restr0.00385

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