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- EMDB-44139: Structure of a complex between Pasteurella multocida surface lipo... -

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Entry
Database: EMDB / ID: EMD-44139
TitleStructure of a complex between Pasteurella multocida surface lipoprotein, PmSLP-1, and bovine complement factor I
Map dataMap of PmSLP-1:FI heterodimer
Sample
  • Complex: Dimeric complex of PmSLP-1 and complement factor I
    • Protein or peptide: Complement factor I
    • Protein or peptide: Pasteurella multocida factor I binding protein, fIbp
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBacterial surface lipoprotein / complement protein / immune evasion / MEMBRANE PROTEIN
Function / homology
Function and homology information


Regulation of Complement cascade / serine-type endopeptidase activity / proteolysis / extracellular region / membrane
Similarity search - Function
: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Factor I / membrane attack complex / factor I membrane attack complex / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich ...: / : / Complement factor I, FIMAC N-terminal domain / Complement factor I, KAZAL domain / Factor I / membrane attack complex / factor I membrane attack complex / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle) / Pasteurella multocida 36950 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsNguyen QH / Norris MJ / Moraes TF
Funding support Canada, United States, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U24GM129547 United States
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, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44139.png

Downloads & links

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Map

FileDownload / File: emd_44139.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of PmSLP-1:FI heterodimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 180 pix.
= 221.94 Å		1.23 Å/pix.
x 180 pix.
= 221.94 Å		1.23 Å/pix.
x 180 pix.
= 221.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.233 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0922
Minimum - Maximum-0.20479164 - 0.45052794
Average (Standard dev.)-0.0017530035 (±0.014453043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 221.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44139_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Conformation 2 of the assembled dimer of PmSLP-1:FI...

Fileemd_44139_additional_1.map
AnnotationConformation 2 of the assembled dimer of PmSLP-1:FI complex prior to symmetry expansion
Projections & Slices
AxesZYX

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Histogram

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Additional map: Conformation 1 of the assembled dimer of PmSLP-1:FI...

Fileemd_44139_additional_2.map
AnnotationConformation 1 of the assembled dimer of PmSLP-1:FI complex prior to symmetry expansion
Projections & Slices
AxesZYX

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Half map: Half Map B

Fileemd_44139_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Half map: Half Map A

Fileemd_44139_half_map_2.map
AnnotationHalf Map A
Projections & Slices
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Sample components

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Entire : Dimeric complex of PmSLP-1 and complement factor I

EntireName: Dimeric complex of PmSLP-1 and complement factor I
Components
  • Complex: Dimeric complex of PmSLP-1 and complement factor I
    • Protein or peptide: Complement factor I
    • Protein or peptide: Pasteurella multocida factor I binding protein, fIbp
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Dimeric complex of PmSLP-1 and complement factor I

SupramoleculeName: Dimeric complex of PmSLP-1 and complement factor I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Pasteurella multocida surface lipoprotein, PmSLP-1, and bovine complement factor I
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Complement factor I

MacromoleculeName: Complement factor I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 66.904922 KDa
SequenceString: EDNFRKRGKS KAVKKSEAHH APEASLSKET EASSEVKPTS TQDTSQKDFV DKKCLTEKHT HLSCNKVFCQ PWQKCIDGTC LCKLPYQCP KNGTRVCSTN GKSYSTYCQQ KSFECYRPEA KFLKSGACTG GGQFSVSLSN GKQDSEGIVA VKLADLDTKM F VCGDSWSI ...String:
EDNFRKRGKS KAVKKSEAHH APEASLSKET EASSEVKPTS TQDTSQKDFV DKKCLTEKHT HLSCNKVFCQ PWQKCIDGTC LCKLPYQCP KNGTRVCSTN GKSYSTYCQQ KSFECYRPEA KFLKSGACTG GGQFSVSLSN GKQDSEGIVA VKLADLDTKM F VCGDSWSI TEANVACIDR GFQLGALDTH RRDPDPNSAE CLHVRCRGLE TSLAECTFTK GVHNSEGLAG VVCYTESAAP PK KDSFQCV NGKRIPQKKA CDGVNDCVDK SDELCCKDCR GEGFLCKSGV CIPKQYKCNG ELDCITGEDE VGCEETGHPE IKE AAEMLT ADMDAERKFT KSFLPKLSCG VKNNMHIRRK RVVGGKPAKM GEFPWQMAIK EGDKIHCGGI YIGGCWILTA AHCV RISRM HRYQIWTSFT DWLRPGFQTV VHSVNRIIIH ENYNGTTYQN DIALIEMKKR PNEKECVLSK SIPACVPWSP YLFQP NDKC IVSGWGREKD NQKVYSLRWG EVHLINNCSE FYPGRYFEKE MQCAGTDDGS IDACKGDSGG PLVCQDVNNV TYVWGV VSW GENCGKSEFP GVYTKVANYF DWISQHVGRS LISQHNI

UniProtKB: Complement factor I

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Macromolecule #2: Pasteurella multocida factor I binding protein, fIbp

MacromoleculeName: Pasteurella multocida factor I binding protein, fIbp / type: protein_or_peptide / ID: 2
Details: Protein sequence includes a short linker, followed by a thrombin cleavage site and 10X His tag. The 10XHis tag was removed.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pasteurella multocida 36950 (bacteria)
Molecular weightTheoretical: 35.247711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKRTVTIPQ AQKVAEKPAL TIQTVVTSPT TPIKAPSLAP TIDTAPKQNP VPTAQITATL PAEPVKVPVL IPEVNKTLLE TSTNPVKDS YNKDAVFTYE LIANPDADYS DQKLILKKEI SYIKLNLGIN QDNKNAPSYI FNLLDDNVYY GFYRDTQDMN R IENKYTYA ...String:
MEKRTVTIPQ AQKVAEKPAL TIQTVVTSPT TPIKAPSLAP TIDTAPKQNP VPTAQITATL PAEPVKVPVL IPEVNKTLLE TSTNPVKDS YNKDAVFTYE LIANPDADYS DQKLILKKEI SYIKLNLGIN QDNKNAPSYI FNLLDDNVYY GFYRDTQDMN R IENKYTYA FKKEAENFDN LQKFNATYEG QFWFSSIDTP NVPTVARAFL TYNNGRVDGE ILAKHWNEKL FQITGFDNNP RK VEIFPTV EYLPNSGTRL TKGATSPHRF QMDLHFINST NGEKNKYLVG QGSTEQYWGV LGMEKKQELA LVPR

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4potassium phosphate monobasic
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5ul of sample was applied to the grid, followed by 5 s blotting.
DetailsSample was purified by gel filtration over a Superdex S200 Increase column

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2335 / Average electron dose: 50.0 e/Å2 / Details: Images were collected at 40-degree tilt
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1938372
Details: Blob picker was used for initial particle selection
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial map comes from ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200426
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.6.1)
DetailsInitial local fitting was done using ChimeraX. Iterative rounds of model building and real-space refinement was done using Coot and PHENIX
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9b3h:
Structure of a complex between Pasteurella multocida surface lipoprotein, PmSLP-1, and bovine complement factor I

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