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- PDB-2vqi: Structure of the P pilus usher (PapC) translocation pore -

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Basic information

Entry
Database: PDB / ID: 2vqi
TitleStructure of the P pilus usher (PapC) translocation pore
ComponentsOUTER MEMBRANE USHER PROTEIN PAPC
KeywordsTRANSPORT / TRANSMEMBRANE / OUTER MEMBRANE / USHER / P PILUS / MEMBRANE / FIMBRIUM / OM TRANSLOCATION PORE / PILUS ASSEMBLY PLATFORM
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
Outer membrane usher protein PapC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsRemaut, H. / Tang, C. / Henderson, N.S. / Pinkner, J.S. / Wang, T. / Hultgren, S.J. / Thanassi, D.G. / Li, H. / Waksman, G.
CitationJournal: Cell / Year: 2008
Title: Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
Authors: Han Remaut / Chunyan Tang / Nadine S Henderson / Jerome S Pinkner / Tao Wang / Scott J Hultgren / David G Thanassi / Gabriel Waksman / Huilin Li /
Abstract: Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the ...Gram-negative pathogens commonly exhibit adhesive pili on their surfaces that mediate specific attachment to the host. A major class of pili is assembled via the chaperone/usher pathway. Here, the structural basis for pilus fiber assembly and secretion performed by the outer membrane assembly platform--the usher--is revealed by the crystal structure of the translocation domain of the P pilus usher PapC and single particle cryo-electron microscopy imaging of the FimD usher bound to a translocating type 1 pilus assembly intermediate. These structures provide molecular snapshots of a twinned-pore translocation machinery in action. Unexpectedly, only one pore is used for secretion, while both usher protomers are used for chaperone-subunit complex recruitment. The translocating pore itself comprises 24 beta strands and is occluded by a folded plug domain, likely gated by a conformationally constrained beta-hairpin. These structures capture the secretion of a virulence factor across the outer membrane of gram-negative bacteria.
History
DepositionMar 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 47-STRANDED BARREL THIS IS REPRESENTED BY A 48-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE USHER PROTEIN PAPC
B: OUTER MEMBRANE USHER PROTEIN PAPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3306
Polymers115,2582
Non-polymers1,0724
Water61334
1
A: OUTER MEMBRANE USHER PROTEIN PAPC
hetero molecules

A: OUTER MEMBRANE USHER PROTEIN PAPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7174
Polymers115,2582
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: OUTER MEMBRANE USHER PROTEIN PAPC
hetero molecules

B: OUTER MEMBRANE USHER PROTEIN PAPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9438
Polymers115,2582
Non-polymers1,6856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)166.500, 101.900, 113.700
Angle α, β, γ (deg.)90.00, 128.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2323, 0.0092, 0.9726), (0.0097, -0.9999, 0.0071), (0.9726, 0.0078, -0.2324)
Vector: 2.7337, 58.9495, -4.5976)

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Components

#1: Protein OUTER MEMBRANE USHER PROTEIN PAPC / PAPC


Mass: 57628.984 Da / Num. of mol.: 2 / Fragment: TRANSLOCATION DOMAIN, RESIDUES 157-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P07110
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONTAINS CENTRAL TRANSLOCATION CHANNEL, RESIDUES 130-640. C-TERMINAL 4 RESIDUES LVPR ...CONSTRUCT CONTAINS CENTRAL TRANSLOCATION CHANNEL, RESIDUES 130-640. C-TERMINAL 4 RESIDUES LVPR RESULT FROM INTRODUCED THROMBIN CLEAVAGE SITE

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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: 3.5 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growpH: 8.5
Details: 5-20 % 3-METHYL-1,5-PENTANEDIOL (MPD), 6-12 % POLYETHYLENE GLYCOL 4000 (PEG4000), 50 MM NA CITRATE PH 5.6, 100 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 48050 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 67.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.2→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5055100.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED ATOMS IN PARTIALLY ORDERED RESIDUES WERE MODELED WITH OCCUPANCY 0.01
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 2410 5 %RANDOM
Rwork0.2593 ---
obs0.2593 47937 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.4143 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.369 Å20 Å219.591 Å2
2---6.277 Å20 Å2
3----1.092 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7517 0 74 34 7625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016733
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.73555
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 384 4.8 %
Rwork0.291 7597 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LDAO.PARAMLDAO.TOPOL
X-RAY DIFFRACTION4C8E4.PARAMC8E4.TOPOL

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