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- PDB-4j3o: Crystal structure of the FimD usher traversed by the pilus tip co... -

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Basic information

Entry
Database: PDB / ID: 4j3o
TitleCrystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH
Components
  • Chaperone protein FimC
  • Outer membrane usher protein FimD
  • Protein FimF
  • Protein FimG
  • Protein FimH
KeywordsCELL ADHESION/CHAPERONE/MEMBRANE PROTEIN / beta barrel / immunglobuline-like fold / type 1 pilus assembly / pilus subunit translocation / adhesion / D-Mannose-binding / bacterial outer membrane / CELL ADHESION-CHAPERONE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : ...fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Outer membrane usher protein FimD, plug domain / Outer membrane usher protein / PapC, C-terminal domain / PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily ...Outer membrane usher protein FimD, plug domain / Outer membrane usher protein / PapC, C-terminal domain / PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein FimF / Protein FimG / Type 1 fimbrin D-mannose specific adhesin / Outer membrane usher protein FimD / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsGeibel, S. / Waksman, G.
CitationJournal: Nature / Year: 2013
Title: Structural and energetic basis of folded-protein transport by the FimD usher.
Authors: Geibel, S. / Procko, E. / Hultgren, S.J. / Baker, D. / Waksman, G.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Protein FimG
H: Protein FimH
C: Chaperone protein FimC
F: Protein FimF
D: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)176,3465
Polymers176,3465
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16540 Å2
ΔGint-45 kcal/mol
Surface area68370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 122.360, 328.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Protein FimG


Mass: 14864.227 Da / Num. of mol.: 1 / Fragment: UNP residues 24-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimG, b4319, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190
#2: Protein Protein FimH


Mass: 29081.314 Da / Num. of mol.: 1 / Fragment: UNP residues 22-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#3: Protein Chaperone protein FimC


Mass: 23582.914 Da / Num. of mol.: 1 / Fragment: UNP residues 37-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#4: Protein Protein FimF


Mass: 16177.095 Da / Num. of mol.: 1 / Fragment: UNP residues 21-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimF, b4318, JW4281 / Production host: Escherichia coli (E. coli) / References: UniProt: P08189
#5: Protein Outer membrane usher protein FimD


Mass: 92640.227 Da / Num. of mol.: 1 / Fragment: UNP residues 46-878
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fimD, b4317, JW5780 / Production host: Escherichia coli (E. coli) / References: UniProt: P30130
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6-2.0M sodium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2010 / Details: mirrors
RadiationMonochromator: Si111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.8→83.67 Å / Num. all: 25518 / Num. obs: 25474 / % possible obs: 99.84 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.8→3.9 Å / % possible all: 99.96

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BWU for FimC:FimF, PDB 3RFZ for FimD, PDB 3JWN for FimG:FimH

3bwu

3rfz

3jwn


Resolution: 3.8→83.668 Å / SU ML: 0.76 / σ(F): 1.33 / Phase error: 37.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2986 1254 4.95 %
Rwork0.2477 --
obs0.2503 25314 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→83.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11732 0 0 0 11732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211974
X-RAY DIFFRACTIONf_angle_d0.45516338
X-RAY DIFFRACTIONf_dihedral_angle_d10.1794225
X-RAY DIFFRACTIONf_chiral_restr0.0321875
X-RAY DIFFRACTIONf_plane_restr0.0022148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8003-3.95250.45861290.41722513X-RAY DIFFRACTION95
3.9525-4.13240.42211390.36362607X-RAY DIFFRACTION100
4.1324-4.35020.37871380.29362634X-RAY DIFFRACTION100
4.3502-4.62280.35621390.24442639X-RAY DIFFRACTION100
4.6228-4.97970.31841400.21662664X-RAY DIFFRACTION100
4.9797-5.48070.32471400.21722669X-RAY DIFFRACTION100
5.4807-6.27350.30651420.23482696X-RAY DIFFRACTION100
6.2735-7.9030.28131450.26032749X-RAY DIFFRACTION100
7.903-83.68770.25441420.23272889X-RAY DIFFRACTION99

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