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Yorodumi- EMDB-75835: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta... -
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Basic information
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| Title | Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 2 | |||||||||
Map data | Non-uniform refinement EMReady Map Sharpening C3bB-Cp60 TED Conformation 2 | |||||||||
Sample |
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Keywords | Complement System / C3 / Alternate Pathway / C3 Pro-Convertase / C3b / Factor B / Compstatin / IMMUNE SYSTEM | |||||||||
| Function / homology | Function and homology informationalternative-complement-pathway C3/C5 convertase / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning ...alternative-complement-pathway C3/C5 convertase / complement binding / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / complement activation, GZMK pathway / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / symbiont cell surface / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / 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 / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / endoplasmic reticulum lumen / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / signaling receptor binding / serine-type endopeptidase activity / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / : / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Herbine K / Lambris J | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: J Med Chem / Year: 2026Title: New Analogs of the Compstatin Family of Clinical Complement Inhibitors with Low Picomolar Target Affinity. Authors: Stephanie A Vogt / Alexander J Lander / Karl Herbine / Ekaterina Umnyakova / Jannes Felsch / Roman Aschwanden / Sarah E Hughes / Oliver Schwardt / Markus A Lill / Martin Smieško / John D ...Authors: Stephanie A Vogt / Alexander J Lander / Karl Herbine / Ekaterina Umnyakova / Jannes Felsch / Roman Aschwanden / Sarah E Hughes / Oliver Schwardt / Markus A Lill / Martin Smieško / John D Lambris / Christina Lamers / Daniel Ricklin / ![]() Abstract: Compstatin-class macrocyclic peptides have emerged as therapeutic complement modulators, with a PEGylated compstatin derivative being approved and sequence-optimized analogs with enhanced PK/PD ...Compstatin-class macrocyclic peptides have emerged as therapeutic complement modulators, with a PEGylated compstatin derivative being approved and sequence-optimized analogs with enhanced PK/PD properties showing clinical promise. By extending structure-activity relationship studies of compstatin, we identified a modification (V3I) that enhances the target affinity up to 30-fold. Analog Cp01-V3I represents the most potent proteinogenic compstatin ( = 20 nM), opening paths toward recombinant applications. Introducing the V3I modification into late-generation compstatin analogs yielded a low-picomolar-affinity derivative ( = 0.08 nM), termed Cp60, featuring potent complement inhibition in vitro. Cryogenic electron microscopy of the C3bB-Cp60 complex at 2.88 Å resolution confirmed the structural basis for enhanced target affinity and provided mechanistic insights. Lastly, we demonstrate that Cp60s ultralong target residence time enables diagnostic applications for detecting complement opsonins on biosurfaces. Collectively, this work highlights the importance of rigorous optimization of de novo peptide inhibitors to improve PK/PD properties and enable novel applications. #1: Journal: To Be PublishedTitle: New analogs of the compstatin family of clinical complement inhibi-tors with low picomolar target affinity Authors: Herbine K / Lambris J | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_75835.map.gz | 143 MB | EMDB map data format | |
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| Header (meta data) | emd-75835-v30.xml emd-75835.xml | 30.5 KB 30.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_75835_fsc.xml | 12.6 KB | Display | FSC data file |
| Images | emd_75835.png | 64.6 KB | ||
| Filedesc metadata | emd-75835.cif.gz | 9.1 KB | ||
| Others | emd_75835_additional_1.map.gz emd_75835_half_map_1.map.gz emd_75835_half_map_2.map.gz | 108.4 MB 200.3 MB 200.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-75835 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-75835 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 11mhMC ![]() 11mgC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_75835.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Non-uniform refinement EMReady Map Sharpening C3bB-Cp60 TED Conformation 2 | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.9343 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: Non-uniform refinement C3bB-Cp60 TED Conformation 2
| File | emd_75835_additional_1.map | ||||||||||||
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| Annotation | Non-uniform refinement C3bB-Cp60 TED Conformation 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Non-uniform refinement (Half Map 2) C3bB-Cp60 TED Conformation 2
| File | emd_75835_half_map_1.map | ||||||||||||
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| Annotation | Non-uniform refinement (Half Map 2) C3bB-Cp60 TED Conformation 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Non-uniform refinement (Half Map 1) C3bB-Cp60 TED Conformation 2
| File | emd_75835_half_map_2.map | ||||||||||||
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| Annotation | Non-uniform refinement (Half Map 1) C3bB-Cp60 TED Conformation 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
-Entire : Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta...
| Entire | Name: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 2 |
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| Components |
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-Supramolecule #1: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compsta...
| Supramolecule | Name: Cryo-EM Structure of Human C3 Pro-Convertase bound to the Compstatin Analog Cp60, TED Conformation 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 256 KDa |
-Macromolecule #1: Complement C3 beta chain
| Macromolecule | Name: Complement C3 beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 71.39332 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 PAA UniProtKB: Complement C3 |
-Macromolecule #2: Complement C3b alpha' chain
| Macromolecule | Name: Complement C3b alpha' chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: Compstatin Cp60
| Macromolecule | Name: Compstatin Cp60 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: synthetic construct (others) |
| Molecular weight | Theoretical: 2.066493 KDa |
| Sequence | String: (DTY)ICI(EXL)QDW(SAR)A HRC(IML)KK |
-Macromolecule #4: Complement factor B
| Macromolecule | Name: Complement factor B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: alternative-complement-pathway C3/C5 convertase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 83.10975 KDa |
| Sequence | String: TPWSLARPQG SCSLEGVEIK GGSFRLLQEG QALEYVCPSG FYPYPVQTRT CRSTGSWSTL KTQDQKTVRK AECRAIHCPR PHDFENGEY WPRSPYYNVS DEISFHCYDG YTLRGSANRT CQVNGRWSGQ TAICDNGAGY CSNPGIPIGT RKVGSQYRLE D SVTYHCSR ...String: TPWSLARPQG SCSLEGVEIK GGSFRLLQEG QALEYVCPSG FYPYPVQTRT CRSTGSWSTL KTQDQKTVRK AECRAIHCPR PHDFENGEY WPRSPYYNVS DEISFHCYDG YTLRGSANRT CQVNGRWSGQ TAICDNGAGY CSNPGIPIGT RKVGSQYRLE D SVTYHCSR GLTLRGSQRR TCQEGGSWSG TEPSCQDSFM YDTPQEVAEA FLSSLTETIE GVDAEDGHGP GEQQKRKIVL DP SGSMNIY LVLDGSDSIG ASNFTGAKKC LVNLIEKVAS YGVKPRYGLV TYATYPKIWV KVSEADSSNA DWVTKQLNEI NYE DHKLKS GTNTKKALQA VYSMMSWPDD VPPEGWNRTR HVIILMTDGL HNMGGDPITV IDEIRDLLYI GKDRKNPRED YLDV YVFGV GPLVNQVNIN ALASKKDNEQ HVFKVKDMEN LEDVFYQMID ESQSLSLCGM VWEHRKGTDY HKQPWQAKIS VIRPS KGHE SCMGAVVSEY FVLTAAHCFT VDDKEHSIKV SVGGEKRDLE IEVVLFHPNY NINGKKEAGI PEFYDYDVAL IKLKNK LKY GQTIRPICLP CTEGTTRALR LPPTTTCQQQ KEELLPAQDI KALFVSEEEK KLTRKEVYIK NGDKKGSCER DAQYAPG YD KVKDISEVVT PRFLCTGGVS PYADPNTCRG DSGGPLIVHK RSRFIQVGVI SWGVVDVCKN QKRQKQVPAH ARDFHINL F QVLPWLKEKL QDEDLGFL UniProtKB: Complement factor B |
-Macromolecule #6: NICKEL (II) ION
| Macromolecule | Name: NICKEL (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: NI |
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| Molecular weight | Theoretical: 58.693 Da |
| Chemical component information | ![]() ChemComp-NI: |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
| Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / 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 |
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Sample preparation
| Concentration | 0.67 mg/mL |
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| Buffer | pH: 7.5 Details: 20 mM Tris-HCl pH 7.5, 140 mM NaCl, and 10 mM NiCl2 |
| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR Details: Negatively glow-discharged with 15 mA for 60 seconds using a PELCO EasiGlow |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
| Details | 3 uM C3b and FB were mixed with Cp60 at 1:1:2 molar ratio in buffer containing 20 mM Tris-HCl pH 7.5, 140 mM NaCl, and 10 mM NiCl2, and incubated on ice for 1 hour prior to vitrification. |
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Electron microscopy
| Microscope | TFS GLACIOS |
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| Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV |
| Software | Name: EPU (ver. 3.14) |
| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 6993 / Average exposure time: 6.0 sec. / Average electron dose: 43.36 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
| Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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| Software | Name: Coot (ver. 0.9.8.96) |
| Details | Initial docking of starting model performed in ChimeraX. Flexible/Refinement performed with Phenix Real-Space Refinement. Coot used for manual fitting and inspection. |
| Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
| Output model | ![]() PDB-11mh: |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
Citation
























Z (Sec.)
Y (Row.)
X (Col.)














































FIELD EMISSION GUN

