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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 / homologyFimbrial-type adhesion domain / Adhesion domain superfamily / Fimbrial-type adhesion domain superfamily / Fimbrial protein / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
Specimen sourceEscherichia coli J96 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4.2 Å resolution
AuthorsHospenthal, M.K. / Costa, T.R.D. / Redzej, A. / Waksman, G.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Nov 29, 2017Structure modelDatabase references / Source and taxonomycitation / entity_src_gen_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

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Structure visualization

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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
Polyers95,0116
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)22260
ΔGint (kcal/M)-80
Surface area (Å2)39350
MethodPISA

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Components

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


Mass: 15835.243 Da / Num. of mol.: 6 / 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 / 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: 1 / 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 mMNaCl1
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
MicroscopyMicroscope model: 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
1RELION2.0particle selection
4GctfCTF correction
9PHENIXmodel refinementreal space refine
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 114.992 deg. / Axial rise/subunit: 8.01188 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 115545
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number 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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