+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42300 | |||||||||
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Title | Structure of the C3bBb-albicin complex | |||||||||
Map data | Main map | |||||||||
Sample |
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Keywords | Complement / Inhibitor / Mosquito / Convertase / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / complement binding / 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 / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Anopheles albimanus (mosquito) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||
Authors | Andersen JF / Lei H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Mechanism of complement inhibition by a mosquito protein revealed through cryo-EM Authors: Andersen JF / Lei H / Strayer EC / Pham V / Ribeiro JM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42300.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-42300-v30.xml emd-42300.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
Images | emd_42300.png | 174.9 KB | ||
Filedesc metadata | emd-42300.cif.gz | 7.5 KB | ||
Others | emd_42300_half_map_1.map.gz emd_42300_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42300 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42300 | HTTPS FTP |
-Related structure data
Related structure data | 8uinMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42300.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_42300_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_42300_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : complex of C3bBb with the inhibitor albicin
Entire | Name: complex of C3bBb with the inhibitor albicin |
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Components |
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-Supramolecule #1: complex of C3bBb with the inhibitor albicin
Supramolecule | Name: complex of C3bBb with the inhibitor albicin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Albicin
Macromolecule | Name: Albicin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Anopheles albimanus (mosquito) |
Molecular weight | Theoretical: 13.461331 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: ANNHIRTVLK LFRTIDLDDS KKSFYLTAAK YGIQTQLREP IIRIVGGYLP STKLSEACVK NMISEVYEIE GDFYSKFSYA CEDHAPYSV ECLEDARDDY LTQLVELFKE TKKCLRE UniProtKB: Secreted protein |
-Macromolecule #2: Complement factor B Bb fragment
Macromolecule | Name: Complement factor B Bb fragment / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.766305 KDa |
Sequence | String: KIVLDPSGSM NIYLVLDGSD SIGASNFTGA KKCLVNLIEK VASYGVKPRY GLVTYATYPK IWVKVSEADS SNADWVTKQL NEINYEDHK LKSGTNTKKA LQAVYSMMSW PDDVPPEGWN RTRHVIILMT DGLHNMGGDP ITVIDEIRDL LYIGKDRKNP R EDYLDVYV ...String: KIVLDPSGSM NIYLVLDGSD SIGASNFTGA KKCLVNLIEK VASYGVKPRY GLVTYATYPK IWVKVSEADS SNADWVTKQL NEINYEDHK LKSGTNTKKA LQAVYSMMSW PDDVPPEGWN RTRHVIILMT DGLHNMGGDP ITVIDEIRDL LYIGKDRKNP R EDYLDVYV FGVGPLVNQV NINALASKKD NEQHVFKVKD MENLEDVFYQ MIDESQSLSL CGMVWEHRKG UniProtKB: Complement factor B |
-Macromolecule #3: Complement C3 beta chain
Macromolecule | Name: Complement C3 beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 71.154047 KDa |
Sequence | String: 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 |
-Macromolecule #4: Complement C3b alpha' chain
Macromolecule | Name: Complement C3b alpha' chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 104.073164 KDa |
Sequence | String: 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 |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 / Details: 10 mM Hepes pH 7.4, 150 mM NaCl, 5 mM MgCl2 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK III |
Details | The sample was formed by incubating C3b, factor B, factor D and albicin. The sample was monodisperse |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.3 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.7 e/Å2 |
-Image processing
Particle selection | Number selected: 492352 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4,0.1) |
Final 3D classification | Number classes: 4 / Software - Name: RELION (ver. 4.0.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1) |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65862 |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||||||||||
Output model | PDB-8uin: |