[English] 日本語
Yorodumi
- EMDB-44146: Conformation 1 of the assembled dimer of PmSLP-1:FI complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44146
TitleConformation 1 of the assembled dimer of PmSLP-1:FI complex
Map dataConformation 1 of the assembled dimer of fIbp:FI
Sample
  • Complex: Dimeric complex of PmSLP-1 and complement factor I
    • Complex: Monomeric complex of PmSLP-1 and complement factor I
      • Complex: Bovine complement factor I
        • Protein or peptide: Bovine complement factor I
      • Complex: Pasteurella multocida factor I binding protein, fIbp
        • Protein or peptide: Pasteurella multocida factor I binding protein, fIbp
KeywordsBacterial surface lipoprotein / complement protein / immune evasion / MEMBRANE PROTEIN
Function / homology
Function and homology information


Regulation of Complement cascade / immune system process / 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: 3.7 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 16, 2025-
Map releaseApr 16, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44146.png

Downloads & links

-
Map

FileDownload / File: emd_44146.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConformation 1 of the assembled dimer of fIbp:FI
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: 0.0732
Minimum - Maximum-0.09221792 - 0.32086277
Average (Standard dev.)-0.0004945756 (±0.013940079)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_44146_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_44146_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44146_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_44146_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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
    • Complex: Monomeric complex of PmSLP-1 and complement factor I
      • Complex: Bovine complement factor I
        • Protein or peptide: Bovine complement factor I
      • Complex: Pasteurella multocida factor I binding protein, fIbp
        • Protein or peptide: Pasteurella multocida factor I binding protein, fIbp

-
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: all
Details: PmSLP-1 was recombinantly expressed and purified from E. coli. Complement factor I was purified from bovine serum. Purified PmSLP-1 and complement factor I were incubated together, and the ...Details: PmSLP-1 was recombinantly expressed and purified from E. coli. Complement factor I was purified from bovine serum. Purified PmSLP-1 and complement factor I were incubated together, and the protein complex was isolated via gel filtration chromatography. The protein complex exists as a dimer (2 copies of PmSLP-1, and 2 copies of complement factor I)
Molecular weightTheoretical: 35 KDa

-
Supramolecule #2: Monomeric complex of PmSLP-1 and complement factor I

SupramoleculeName: Monomeric complex of PmSLP-1 and complement factor I / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

-
Supramolecule #3: Bovine complement factor I

SupramoleculeName: Bovine complement factor I / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1 / Details: Complement factor I purified from bovine serum
Source (natural)Organism: Bos taurus (domestic cattle)

-
Supramolecule #4: Pasteurella multocida factor I binding protein, fIbp

SupramoleculeName: Pasteurella multocida factor I binding protein, fIbp / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2
Details: fIbp is a surface lipoprotein from Pasteurella multocida. The protein was expressed and purified from E. coli
Source (natural)Organism: Pasteurella multocida 36950 (bacteria)

-
Macromolecule #1: Bovine complement factor I

MacromoleculeName: Bovine complement factor I / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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

-
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.
Enantiomer: LEVO
Source (natural)Organism: Pasteurella multocida 36950 (bacteria)
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119048
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more