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- PDB-1ze3: Crystal Structure of the Ternary Complex of FIMD (N-Terminal Doma... -

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Basic information

Entry
Database: PDB / ID: 1ze3
TitleCrystal Structure of the Ternary Complex of FIMD (N-Terminal Domain) with FIMC and the Pilin Domain of FIMH
Components
  • Chaperone protein fimC
  • FimH protein
  • Outer membrane usher protein fimD
KeywordsCHAPERONE/STRUCTURAL/MEMBRANE PROTEIN / Usher / soluble domain / ternary complex with chaperone and pilus subunit / CHAPERONE-STRUCTURAL-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
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 ...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
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: 1.84 Å
AuthorsNishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Grutter, M.G. / Wuthrich, K. ...Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Grutter, M.G. / Wuthrich, K. / Glockshuber, R. / Capitani, G.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD.
Authors: Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Glockshuber, R. / Capitani, G.
History
DepositionApr 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
C: Chaperone protein fimC
H: FimH protein
D: Outer membrane usher protein fimD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,44715
Polymers48,7023
Non-polymers74512
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint8 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.820, 83.320, 110.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chaperone protein fimC


Mass: 22754.031 Da / Num. of mol.: 1 / Fragment: FimC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC / Plasmid: pCT-FimH-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P31697
#2: Protein FimH protein


Mass: 12283.583 Da / Num. of mol.: 1 / Fragment: FimH pilin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: pCT-FimH-FimC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#3: Protein Outer membrane usher protein fimD


Mass: 13664.263 Da / Num. of mol.: 1 / Fragment: FimD N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Plasmid: pFimDn (1-125) / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P30130
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 6000, MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.843→33.615 Å / Num. obs: 44185 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 15
Reflection shellResolution: 1.84→1.91 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.363 / % possible all: 99.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL DERIVED FROM PDB ENTRY 1QUN

1qun


Resolution: 1.84→33.7 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 895 RANDOM
Rwork0.19 --
obs-44185 -
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.997 Å20 Å20 Å2
2---0.04 Å20 Å2
3---2.037 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.84→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 48 510 3933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.84→1.91 Å
RfactorNum. reflection
Rfree0.266 98
Rwork0.247 -
obs-4013

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