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- PDB-6bea: Crystal structure of the autotransporter UpaB from E. coli strain... -

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Basic information

Entry
Database: PDB / ID: 6bea
TitleCrystal structure of the autotransporter UpaB from E. coli strain CFT073
ComponentsAutotransporter protein UpaBAuto carrier
KeywordsPROTEIN BINDING / autotransporter protein / bacterial adhesin / virulence factor / fibronectin / glycosaminoglycan
Function / homology
Function and homology information


Pertactin virulence factor family / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Autotransporter domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.97 Å
AuthorsPaxman, J.J. / Heras, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150102287 Australia
Australian Research Council (ARC)FT130100580 Australia
Australian Synchrotron Research Program Fellowship Australia
CitationJournal: Nat Commun / Year: 2019
Title: Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules.
Authors: Jason J Paxman / Alvin W Lo / Matthew J Sullivan / Santosh Panjikar / Michael Kuiper / Andrew E Whitten / Geqing Wang / Chi-Hao Luan / Danilo G Moriel / Lendl Tan / Kate M Peters / Minh-Duy ...Authors: Jason J Paxman / Alvin W Lo / Matthew J Sullivan / Santosh Panjikar / Michael Kuiper / Andrew E Whitten / Geqing Wang / Chi-Hao Luan / Danilo G Moriel / Lendl Tan / Kate M Peters / Minh-Duy Phan / Christine L Gee / Glen C Ulett / Mark A Schembri / Begoña Heras /
Abstract: Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation ...Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autotransporter protein UpaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,66911
Polymers47,7311
Non-polymers93710
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, We also performed Sedimentation Velocity Analytical Ultracentrifugation experiments. SAXS and AUC showed that UpaB is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-30 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.611, 68.611, 165.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Autotransporter protein UpaB / Auto carrier


Mass: 47731.375 Da / Num. of mol.: 1 / Fragment: UNP residues 37-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: c0426 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 pLysS / References: UniProt: A0A0H2V5A3

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Non-polymers , 7 types, 250 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.8
Details: 0.1 M sodium acetate, 0.2 M ammonium sulfate, 28% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 32914 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.44 Å2 / Rmerge(I) obs: 0.14 / Χ2: 1.12 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.97-2.046.80.88132191.105199.6
2.04-2.127.30.70132121.187199.8
2.12-2.227.60.50732801.1131100
2.22-2.347.60.38232021.0961100
2.34-2.487.60.34232801.1571100
2.48-2.677.60.27332601.151100
2.67-2.947.60.18632731.081100
2.94-3.377.50.1233101.0741100
3.37-4.247.40.09233591.0971100
4.24-5070.05635191.146199.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
SHELXDEphasing
ARP/wARPmodel building
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.97→40.437 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2185 1667 5.08 %
Rwork0.1746 --
obs0.1768 32811 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 30.9616 Å2 / Biso min: 14.64 Å2
Refinement stepCycle: final / Resolution: 1.97→40.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 45 240 3406
Biso mean--54.74 40.41 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073226
X-RAY DIFFRACTIONf_angle_d0.8964388
X-RAY DIFFRACTIONf_chiral_restr0.061537
X-RAY DIFFRACTIONf_plane_restr0.004575
X-RAY DIFFRACTIONf_dihedral_angle_d3.8542521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9675-2.02540.25091200.21792537265799
2.0254-2.09080.27131470.21125402687100
2.0908-2.16550.22951490.197225452694100
2.1655-2.25220.27621240.193925432667100
2.2522-2.35470.26111290.186125922721100
2.3547-2.47880.25481240.188425912715100
2.4788-2.63410.24051560.181725712727100
2.6341-2.83750.22211430.174625822725100
2.8375-3.12290.20391480.162525932741100
3.1229-3.57460.1981570.156525942751100
3.5746-4.50260.20041170.143826752792100
4.5026-40.44590.19551530.1882781293499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23580.2718-0.26470.53380.33630.5065-0.09860.09930.0186-0.04080.06190.0462-0.1031-0.001300.16330.0277-0.01440.20820.00430.16881.405644.7761-13.2683
2-0.0588-0.03790.03250.47-0.08580.28190.02380.01320.007-0.0059-0.04-0.0469-0.00470.0207-00.16870.02140.00110.190.01840.179510.059256.07813.0803
30.149-0.0021-0.03640.01240.00170.1092-0.0097-0.04330.0660.2257-0.0202-0.0321-0.06690.082300.3747-0.0097-0.05250.22220.01990.246617.43152.343943.7111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 191 )A40 - 191
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 420 )A192 - 420
3X-RAY DIFFRACTION3chain 'A' and (resid 421 through 472 )A421 - 472

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