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- EMDB-42244: Complex of C3b with the inhibitor albicin -

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Basic information

Entry
Database: EMDB / ID: EMD-42244
TitleComplex of C3b with the inhibitor albicin
Map datamain map
Sample
  • Complex: C3b-albicin dimeric complex
    • Complex: Albicin
      • Protein or peptide: Albicin
    • Complex: Complement C3 beta chain, Complement C3b alpha' chain
      • Protein or peptide: Complement C3 beta chain
      • Protein or peptide: Complement C3b alpha' chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplement / Mosquito / C3 / convertase / alternative pathway / 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 / Peptide ligand-binding receptors / complement activation, classical pathway / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / 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) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / immune 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 / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / 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 / : ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / 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
Secreted protein / Complement C3
Similarity search - Component
Biological speciesAnopheles albimanus (mosquito) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsAndersen JF / Lei H / Strayer E / Ribeiro JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: The mechanism of a mosquito salivary inhibitor of the alternative C3 convertase is elucidated through structural analysis of its complex with C3bBb
Authors: Andersen JF / Lei H / Strayer E / Pham V / Ribeiro JM
History
DepositionOct 6, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42244.png

Downloads & links

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Map

FileDownload / File: emd_42244.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.069
Minimum - Maximum-0.69059795 - 1.0459887
Average (Standard dev.)0.00096194557 (±0.02745318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_42244_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_42244_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C3b-albicin dimeric complex

EntireName: C3b-albicin dimeric complex
Components
  • Complex: C3b-albicin dimeric complex
    • Complex: Albicin
      • Protein or peptide: Albicin
    • Complex: Complement C3 beta chain, Complement C3b alpha' chain
      • Protein or peptide: Complement C3 beta chain
      • Protein or peptide: Complement C3b alpha' chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: C3b-albicin dimeric complex

SupramoleculeName: C3b-albicin dimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Albicin

SupramoleculeName: Albicin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Anopheles albimanus (mosquito)

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Supramolecule #3: Complement C3 beta chain, Complement C3b alpha' chain

SupramoleculeName: Complement C3 beta chain, Complement C3b alpha' chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Albicin

MacromoleculeName: Albicin / type: protein_or_peptide / ID: 1 / Details: Inhibitor of complement / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anopheles albimanus (mosquito)
Molecular weightTheoretical: 13.461331 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ANNHIRTVLK LFRTIDLDDS KKSFYLTAAK YGIQTQLREP IIRIVGGYLP STKLSEACVK NMISEVYEIE GDFYSKFSYA CEDHAPYSV ECLEDARDDY LTQLVELFKE TKKCLRE

UniProtKB: Secreted protein

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Macromolecule #2: Complement C3 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.154047 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

UniProtKB: Complement C3

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Macromolecule #3: Complement C3b alpha' chain

MacromoleculeName: Complement C3b alpha' chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.073164 KDa
SequenceString: SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV ...String:
SNLDEDIIAE ENIVSRSEFP ESWLWNVEDL KEPPKNGIST KLMNIFLKDS ITTWEILAVS MSDKKGICVA DPFEVTVMQD FFIDLRLPY SVVRNEQVEI RAVLYNYRQN QELKVRVELL HNPAFCSLAT TKRRHQQTVT IPPKSSLSVP YVIVPLKTGL Q EVEVKAAV YHHFISDGVR KSLKVVPEGI RMNKTVAVRT LDPERLGREG VQKEDIPPAD LSDQVPDTES ETRILLQGTP VA QMTEDAV DAERLKHLIV TPSGCGEQNM IGMTPTVIAV HYLDETEQWE KFGLEKRQGA LELIKKGYTQ QLAFRQPSSA FAA FVKRAP STWLTAYVVK VFSLAVNLIA IDSQVLCGAV KWLILEKQKP DGVFQEDAPV IHQEMIGGLR NNNEKDMALT AFVL ISLQE AKDICEEQVN SLPGSITKAG DFLEANYMNL QRSYTVAIAG YALAQMGRLK GPLLNKFLTT AKDKNRWEDP GKQLY NVEA TSYALLALLQ LKDFDFVPPV VRWLNEQRYY GGGYGSTQAT FMVFQALAQY QKDAPDHQEL NLDVSLQLPS RSSKIT HRI HWESASLLRS EETKENEGFT VTAEGKGQGT LSVVTMYHAK AKDQLTCNKF DLKVTIKPAP ETEKRPQDAK NTMILEI CT RYRGDQDATM SILDISMMTG FAPDTDDLKQ LANGVDRYIS KYELDKAFSD RNTLIIYLDK VSHSEDDCLA FKVHQYFN V ELIQPGAVKV YAYYNLEESC TRFYHPEKED GKLNKLCRDE LCRCAEENCF IQKSDDKVTL EERLDKACEP GVDYVYKTR LVKVQLSNDF DEYIMAIEQT IKSGSDEVQV GQQRTFISPI KCREALKLEE KKHYLMWGLS SDFWGEKPNL SYIIGKDTWV EHWPEEDEC QDEENQKQCQ DLGAFTESMV VFGCPN

UniProtKB: Complement C3

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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: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
DetailsComplex was formed by incubation of C3b, Factor B, Factor D and albicin in vitro and was monodisperse

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.7 e/Å2

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Image processing

Particle selectionNumber selected: 147624
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rur

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: RELION (ver. 4.0.1), cryoSPARC (ver. 3.3.1))
Number images used: 52781

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