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

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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
Specimen sourceEscherichia coli j96 / bacteria / image: Escherichia coli
MethodElectron microscopy (4.2 Å resolution / Helical array / Helical)
AuthorsHospenthal, M.K. / Costa, T.R.D. / Redzej, A. / Waksman, G.
CitationStructure, 2017, 25, 1829-1838.e4

Structure, 2017, 25, 1829-1838.e4 Yorodumi Papers
The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.
Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman

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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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

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


#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 / image: Escherichia coli
Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli HB101 / References: UniProt: P04128

Experimental details


EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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
Source (recombinant)Organism: Escherichia coli HB101
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameBuffer ID
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 %

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 FIELD
Image recordingElectron dose: 1.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: dev_2776: / Classification: refinement
EM software
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
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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