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- PDB-9b3e: Crystal structure of a Slam-dependent surface lipoprotein, PmSLP,... -

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Basic information

Entry
Database: PDB / ID: 9b3e
TitleCrystal structure of a Slam-dependent surface lipoprotein, PmSLP, in Pasteurella multocida
Componentssurface lipoprotein, PmSLP-1
KeywordsMEMBRANE PROTEIN / Bacterial surface lipoprotein / complement evasion
Function / homologySELENIUM ATOM
Function and homology information
Biological speciesPasteurella multocida 36950 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLai, C.H.R. / Shah, M. / Nguyen, Q.H. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
CitationJournal: PLoS Pathog / Year: 2025
Title: A surface lipoprotein on Pasteurella multocida binds complement factor I to promote immune evasion.
Authors: Quynh Huong Nguyen / Chun Heng Royce Lai / Michael J Norris / Dixon Ng / Megha Shah / Christine Chieh-Lin Lai / David E Isenman / Trevor F Moraes /
Abstract: Pasteurella multocida is the leading cause of wound infections in humans following animals' bites or scratches. This bacterium is also commonly found in the respiratory tract of many mammals and can ...Pasteurella multocida is the leading cause of wound infections in humans following animals' bites or scratches. This bacterium is also commonly found in the respiratory tract of many mammals and can cause serious diseases resulting in the rapid death of infected animals, especially cattle. To prevent these infections in cattle, a subunit-based vaccine utilizing the surface lipoprotein PmSLP was developed and showed remarkable protection with a single dose administration. Here, we report that PmSLP binds host complement factor I (FI) and facilitates cleavage of complement components C3b and C4b independently of any cofactors (e.g., FH, C4BP), thereby allowing the pathogen to evade host defence. Cryo-EM structure of PmSLP bound to FI reveals that PmSLP stimulates FI enzymatic activity by stabilizing the catalytic domain. This is the first time that a bacterial protein has been shown to directly activate FI independent of complement cofactors and target all arms of the complement cascade.
History
DepositionMar 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: surface lipoprotein, PmSLP-1
B: surface lipoprotein, PmSLP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3053
Polymers57,2262
Non-polymers791
Water3,693205
1
A: surface lipoprotein, PmSLP-1


Theoretical massNumber of molelcules
Total (without water)28,6131
Polymers28,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: surface lipoprotein, PmSLP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6922
Polymers28,6131
Non-polymers791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.910, 81.500, 109.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein surface lipoprotein, PmSLP-1


Mass: 28613.104 Da / Num. of mol.: 2 / Mutation: E222A, K223A, and K224A
Source method: isolated from a genetically manipulated source
Details: The protein construct contains a linker region, thrombin cleavage site, and a 10X His tag at the C-terminus. The His tag is removed by thrombin after the affinity purification step.
Source: (gene. exp.) Pasteurella multocida 36950 (bacteria) / Gene: AET16641.1 / Plasmid: pET52 / Production host: Escherichia coli (E. coli) / Strain (production host): T7SHuffle
#2: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na cacodylate, ammonium tartrate, PEG3350

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→47.744 Å / Num. obs: 67811 / % possible obs: 98.15 % / Redundancy: 6.4 % / Biso Wilson estimate: 36.89 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Net I/σ(I): 11.96
Reflection shellResolution: 2→2.071 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.366 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 3359 / CC1/2: 0.746 / CC star: 0.924 / Rpim(I) all: 0.5811 / % possible all: 93.07

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.13-2998phasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→47.74 Å / SU ML: 0.3137 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 28.8062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 3410 5.03 %
Rwork0.2034 64395 -
obs0.2055 67805 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.86 Å2
Refinement stepCycle: LAST / Resolution: 2→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 1 205 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793585
X-RAY DIFFRACTIONf_angle_d0.89164856
X-RAY DIFFRACTIONf_chiral_restr0.0549504
X-RAY DIFFRACTIONf_plane_restr0.0055639
X-RAY DIFFRACTIONf_dihedral_angle_d6.1845466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.38221480.342777X-RAY DIFFRACTION100
2.03-2.060.46461190.37952258X-RAY DIFFRACTION83.73
2.06-2.090.5941310.4992496X-RAY DIFFRACTION90.18
2.09-2.130.35071480.32112720X-RAY DIFFRACTION99.86
2.13-2.160.32961420.30862714X-RAY DIFFRACTION99.79
2.16-2.20.30661480.28912754X-RAY DIFFRACTION99.66
2.2-2.240.40491370.34422529X-RAY DIFFRACTION93.77
2.24-2.290.39431370.35122678X-RAY DIFFRACTION97.2
2.29-2.340.27831460.2572730X-RAY DIFFRACTION100
2.34-2.390.27071390.23842755X-RAY DIFFRACTION99.83
2.39-2.450.29871440.22682707X-RAY DIFFRACTION99.93
2.45-2.520.32281460.23212714X-RAY DIFFRACTION99.9
2.52-2.590.26941430.22682726X-RAY DIFFRACTION99.9
2.59-2.680.27181440.2332723X-RAY DIFFRACTION99.86
2.68-2.770.27751460.21252738X-RAY DIFFRACTION99.97
2.77-2.880.24351410.21132732X-RAY DIFFRACTION100
2.88-3.020.27131440.20672737X-RAY DIFFRACTION99.97
3.02-3.170.23351450.19412717X-RAY DIFFRACTION99.97
3.17-3.370.25651430.19062732X-RAY DIFFRACTION99.76
3.37-3.630.24891390.16472719X-RAY DIFFRACTION99.69
3.63-40.19161480.15862724X-RAY DIFFRACTION99.21
4-4.580.17411480.13842731X-RAY DIFFRACTION99.48
4.58-5.770.18341440.15812684X-RAY DIFFRACTION98.47
5.77-47.740.19511400.18932600X-RAY DIFFRACTION95.37
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)
11.03097178185-0.168840805867-0.9734935003952.22584467062-1.85224691665.803588526550.060685611016-0.1329752770470.06058062839720.1193004759940.001563234593880.0455254113664-0.2739781216780.41375439915-0.04394416836190.271738969541-0.051114240825-0.01573366500620.295948092694-0.05257739924410.25013353378418.65352.77379.991
21.351153499220.7614827367710.2392420647853.51355587817-0.2142380775242.808262534550.0708540017115-0.0123047152550.116429210311-0.171695414543-0.1065485821860.319939869021-0.01981801361780.02279521290550.0154317162420.2218225944310.0257647706265-0.005141085314050.289793474792-0.05629052604190.27800960663313.72648.17661.9
34.43992763115-0.666725435266-2.50290934782.126546561870.7069316376814.011646988020.05792823292990.1030078611110.1127677128740.2115399730880.0110662107510.0226734822407-0.21914680642-0.332810638688-0.08993112423960.276080197408-0.00136166020229-0.01895689173170.268484515875-0.006376684952460.236149473114-3.1412.59163.276
42.33025183742-0.303180433316-0.7951349584064.401847305780.5310703489161.824545842240.114685916003-0.246483446661-0.245588266090.6877443878460.0390336885031-0.7781212394280.1336885663150.305342432243-0.08925813226180.3711928265660.0276308010383-0.1645041663570.324894187386-0.001530357411370.4552172728418.27112.62367.125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 103:196 )A103 - 196
2X-RAY DIFFRACTION2( CHAIN A AND RESID 197:318 )A197 - 318
3X-RAY DIFFRACTION3( CHAIN B AND RESID 102:175 )B102 - 175
4X-RAY DIFFRACTION4( CHAIN B AND RESID 176:317 )B176 - 317

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