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- EMDB-14707: Trypanosoma brucei gambiense ISG65 in complex with human compleme... -

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Entry
Database: EMDB / ID: EMD-14707
TitleTrypanosoma brucei gambiense ISG65 in complex with human complement component C3
Map data
Sample
  • Complex: Trypanosoma brucei gambiense ISG65 in complex with human complement component C3
    • Complex: Complement C3 beta chain
      • Protein or peptide: Complement C3 beta chain
    • Complex: 65 kDa invariant surface glycoprotein
      • Protein or peptide: 65 kDa invariant surface glycoprotein, putative
    • Complex: Complement C3 alpha chain
      • Protein or peptide: Complement C3Complement component 3
Keywordscomplement / complex / IMMUNE SYSTEM
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / azurophil granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Trypanosome invariant surface glycoprotein / Invariant surface glycoprotein / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 ...Trypanosome invariant surface glycoprotein / Invariant surface glycoprotein / : / : / Complement component 3, CUB domain 2 / Complement component 3, CUB domain 1 / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
65 kDa invariant surface glycoprotein, putative / Complement C3
Similarity search - Component
Biological speciesHomo sapiens (human) / Trypanosoma brucei gambiense (eukaryote) / Homo Sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsSuelzen H / Zoll S
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic22-21612S Czech Republic
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of Trypanosoma brucei gambiense ISG65 with human complement C3 and C3b and their roles in alternative pathway restriction.
Authors: Hagen Sülzen / Jakub Began / Arun Dhillon / Sami Kereïche / Petr Pompach / Jitka Votrubova / Farnaz Zahedifard / Adriana Šubrtova / Marie Šafner / Martin Hubalek / Maaike Thompson / ...Authors: Hagen Sülzen / Jakub Began / Arun Dhillon / Sami Kereïche / Petr Pompach / Jitka Votrubova / Farnaz Zahedifard / Adriana Šubrtova / Marie Šafner / Martin Hubalek / Maaike Thompson / Martin Zoltner / Sebastian Zoll /
Abstract: African Trypanosomes have developed elaborate mechanisms to escape the adaptive immune response, but little is known about complement evasion particularly at the early stage of infection. Here we ...African Trypanosomes have developed elaborate mechanisms to escape the adaptive immune response, but little is known about complement evasion particularly at the early stage of infection. Here we show that ISG65 of the human-infective parasite Trypanosoma brucei gambiense is a receptor for human complement factor C3 and its activation fragments and that it takes over a role in selective inhibition of the alternative pathway C5 convertase and thus abrogation of the terminal pathway. No deposition of C4b, as part of the classical and lectin pathway convertases, was detected on trypanosomes. We present the cryo-electron microscopy (EM) structures of native C3 and C3b in complex with ISG65 which reveal a set of modes of complement interaction. Based on these findings, we propose a model for receptor-ligand interactions as they occur at the plasma membrane of blood-stage trypanosomes and may facilitate innate immune escape of the parasite.
History
DepositionApr 3, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14707.png

Downloads & links

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Map

FileDownload / File: emd_14707.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21823613 - 0.41306058
Average (Standard dev.)0.00004076337 (±0.008736622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14707_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14707_half_map_2.map
Projections & Slices
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Sample components

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Entire : Trypanosoma brucei gambiense ISG65 in complex with human compleme...

EntireName: Trypanosoma brucei gambiense ISG65 in complex with human complement component C3
Components
  • Complex: Trypanosoma brucei gambiense ISG65 in complex with human complement component C3
    • Complex: Complement C3 beta chain
      • Protein or peptide: Complement C3 beta chain
    • Complex: 65 kDa invariant surface glycoprotein
      • Protein or peptide: 65 kDa invariant surface glycoprotein, putative
    • Complex: Complement C3 alpha chain
      • Protein or peptide: Complement C3Complement component 3

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Supramolecule #1: Trypanosoma brucei gambiense ISG65 in complex with human compleme...

SupramoleculeName: Trypanosoma brucei gambiense ISG65 in complex with human complement component C3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Complement C3 beta chain

SupramoleculeName: Complement C3 beta chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 65 kDa invariant surface glycoprotein

SupramoleculeName: 65 kDa invariant surface glycoprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Trypanosoma brucei gambiense (eukaryote)

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Supramolecule #4: Complement C3 alpha chain

SupramoleculeName: Complement C3 alpha chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo Sapiens (human)

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Macromolecule #1: Complement C3 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.39332 KDa
SequenceString: SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP ...String:
SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVHDF PGKKLVLSSE KTVLTPATNH MGNVTFTIPA NREFKSEKGR NKFVTVQAT FGTQVVEKVV LVSLQSGYLF IQTDKTIYTP GSTVLYRIFT VNHKLLPVGR TVMVNIENPE GIPVKQDSLS S QNQLGVLP LSWDIPELVN MGQWKIRAYY ENSPQQVFST EFEVKEYVLP SFEVIVEPTE KFYYIYNEKG LEVTITARFL YG KKVEGTA FVIFGIQDGE QRISLPESLK RIPIEDGSGE VVLSRKVLLD GVQNPRAEDL VGKSLYVSAT VILHSGSDMV QAE RSGIPI VTSPYQIHFT KTPKYFKPGM PFDLMVFVTN PDGSPAYRVP VAVQGEDTVQ SLTQGDGVAK LSINTHPSQK PLSI TVRTK KQELSEAEQA TRTMQALPYS TVGNSNNYLH LSVLRTELRP GETLNVNFLL RMDRAHEAKI RYYTYLIMNK GRLLK AGRQ VREPGQDLVV LPLSITTDFI PSFRLVAYYT LIGASGQREV VADSVWVDVK DSCVGSLVVK SGQSEDRQPV PGQQMT LKI EGDHGARVVL VAVDKGVFVL NKKNKLTQSK IWDVVEKADI GCTPGSGKDY AGVFSDAGLT FTSSSGQQTA QRAELQC PQ PAA

UniProtKB: Complement C3

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Macromolecule #2: Complement C3

MacromoleculeName: Complement C3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.169875 KDa
SequenceString: SVQLTEKRMD KVGKYPKELR KCCEDGMREN PMRFSCQRRT RFISLGEACK KVFLDCCNYI TELRRQHARA SHLGLARSNL DEDIIAEEN IVSRSEFPES WLWNVEDLKE PPKNGISTKL MNIFLKDSIT TWEILAVSMS DKKGICVADP FEVTVMQDFF I DLRLPYSV ...String:
SVQLTEKRMD KVGKYPKELR KCCEDGMREN PMRFSCQRRT RFISLGEACK KVFLDCCNYI TELRRQHARA SHLGLARSNL DEDIIAEEN IVSRSEFPES WLWNVEDLKE PPKNGISTKL MNIFLKDSIT TWEILAVSMS DKKGICVADP FEVTVMQDFF I DLRLPYSV VRNEQVEIRA VLYNYRQNQE LKVRVELLHN PAFCSLATTK RRHQQTVTIP PKSSLSVPYV IVPLKTGLQE VE VKAAVYH HFISDGVRKS LKVVPEGIRM NKTVAVRTLD PERLGREGVQ KEDIPPADLS DQVPDTESET RILLQGTPVA QMT EDAVDA ERLKHLIVTP SGCGEQNMIG MTPTVIAVHY LDETEQWEKF GLEKRQGALE LIKKGYTQQL AFRQPSSAFA AFVK RAPST WLTAYVVKVF SLAVNLIAID SQVLCGAVKW LILEKQKPDG VFQEDAPVIH QEMIGGLRNN NEKDMALTAF VLISL QEAK DICEEQVNSL PGSITKAGDF LEANYMNLQR SYTVAIAGYA LAQMGRLKGP LLNKFLTTAK DKNRWEDPGK QLYNVE ATS YALLALLQLK DFDFVPPVVR WLNEQRYYGG GYGSTQATFM VFQALAQYQK DAPDHQELNL DVSLQLPSRS SKITHRI HW ESASLLRSEE TKENEGFTVT AEGKGQGTLS VVTMYHAKAK DQLTCNKFDL KVTIKPAPET EKRPQDAKNT MILEICTR Y RGDQDATMSI LDISMMTGFA PDTDDLKQLA NGVDRYISKY ELDKAFSDRN TLIIYLDKVS HSEDDCLAFK VHQYFNVEL IQPGAVKVYA YYNLEESCTR FYHPEKEDGK LNKLCRDELC RCAEENCFIQ KSDDKVTLEE RLDKACEPGV DYVYKTRLVK VQLSNDFDE YIMAIEQTIK SGSDEVQVGQ QRTFISPIKC REALKLEEKK HYLMWGLSSD FWGEKPNLSY IIGKDTWVEH W PEEDECQD EENQKQCQDL GAFTESMVVF GCPN

UniProtKB: Complement C3

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Macromolecule #3: 65 kDa invariant surface glycoprotein, putative

MacromoleculeName: 65 kDa invariant surface glycoprotein, putative / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei gambiense (eukaryote) / Strain: MHOM/CI/86/DAL972
Molecular weightTheoretical: 40.823516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MLLVIGSEDN RVPGDKKLTK EGAAALCKMK HLADKVAKER SQELKDRTQN FAGYIEFELY RIDYWLEKL NGPKGRKDGY AKLSDSDIEK VKEIFNKAKD GITKQLPEAK KAGEEAGKLH TEVKKAAENA RGQDLDDDTA K STGLYRVL ...String:
MGSSHHHHHH SSGLVPRGSH MLLVIGSEDN RVPGDKKLTK EGAAALCKMK HLADKVAKER SQELKDRTQN FAGYIEFELY RIDYWLEKL NGPKGRKDGY AKLSDSDIEK VKEIFNKAKD GITKQLPEAK KAGEEAGKLH TEVKKAAENA RGQDLDDDTA K STGLYRVL NWYCITKEER HNATPNCDGI QFRKHYLSVN RSAIDCSSTS YEENYDWSAN ALQVALNSWE DVKPKKLESA GS DKNCNIG QSSESHPCTM TEEWQTPYKE TVEKLRELED AYQRGKKAHD AMLGYANTAY AVNTKVEQEK PLTEVIAAAK EAG KKGAKI IIPAAAPATP TNSTKNDDSA PTEHVDRGIA TNETQVEVGI D

UniProtKB: 65 kDa invariant surface glycoprotein, putative

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloridesodium chloride
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2a73

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 406545
FSC plot (resolution estimation)

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