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- PDB-5oh0: The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Us... -

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Basic information

Entry
Database: PDB / ID: 5oh0
TitleThe Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
ComponentsType-1 fimbrial protein, A chain
KeywordsPROTEIN FIBRIL / bacterial pilus / chaperone-usher pilus
Function / homologycell adhesion involved in single-species biofilm formation / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
Biological speciesEscherichia coli J96 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHospenthal, M.K. / Costa, T.R.D. / Redzej, A. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)018434 United Kingdom
CitationJournal: Structure / Year: 2017
Title: The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.
Authors: Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman /
Abstract: Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play ...Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Assembly

Deposited unit
A: Type-1 fimbrial protein, A chain
B: Type-1 fimbrial protein, A chain
C: Type-1 fimbrial protein, A chain
D: Type-1 fimbrial protein, A chain
E: Type-1 fimbrial protein, A chain
F: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)95,0116
Polymers95,0116
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22260 Å2
ΔGint-80 kcal/mol
Surface area39350 Å2
MethodPISA

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Components

#1: Protein
Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15835.243 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli J96 (bacteria) / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: P04128

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Type 1 Chaperone-usher pilus / Type: COMPLEX
Details: Superhelical assembly of the pilus rod subunit FimA
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli J96 (bacteria)
Source (recombinant)Organism: Escherichia coli HB101 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2150 mMNaClSodium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil 1.2/1.3 400 mesh grid
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2776: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION2particle selection
4GctfCTF correction
9PHENIXmodel refinementreal space refine
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 114.992 ° / Axial rise/subunit: 8.01188 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 115545
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115510 / Symmetry type: HELICAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
12JTYA120-159
22JTYA1172-182
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036666
ELECTRON MICROSCOPYf_angle_d0.6189114
ELECTRON MICROSCOPYf_dihedral_angle_d7.7553864
ELECTRON MICROSCOPYf_chiral_restr0.0471140
ELECTRON MICROSCOPYf_plane_restr0.0041218

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