+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22328 | |||||||||
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Title | IgA1 Protease in complex with neutralizing mAbIgA-specific metalloendopeptidase | |||||||||
Map data | IgA1 Protease with mAb | |||||||||
Sample |
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Function / homology | Function and homology information IgA-specific metalloendopeptidase / cell wall / metalloendopeptidase activity / membrane => GO:0016020 / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Eisenmesser EZ / Zheng H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease. Authors: Zhiming Wang / Jeremy Rahkola / Jasmina S Redzic / Ying-Chih Chi / Norman Tran / Todd Holyoak / Hongjin Zheng / Edward Janoff / Elan Eisenmesser / Abstract: Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since ...Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since their discovery nearly 30 years ago despite the potential for developing vaccines that target these enzymes to block infection. Here we show through a series of cryo-electron microscopy single particle reconstructions how the Streptococcus pneumoniae IgA1 protease facilitates IgA1 substrate recognition and how this can be inhibited. Specifically, the Streptococcus pneumoniae IgA1 protease subscribes to an active-site-gated mechanism where a domain undergoes a 10.0 Å movement to facilitate cleavage. Monoclonal antibody binding inhibits this conformational change, providing a direct means to block infection at the host interface. These structural studies explain decades of biological and biochemical studies and provides a general strategy to block Streptococcus pneumoniae IgA1 protease activity to potentially prevent infection. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22328.map.gz | 122.3 MB | EMDB map data format | |
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Header (meta data) | emd-22328-v30.xml emd-22328.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_22328.png | 72.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22328 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22328 | HTTPS FTP |
-Related structure data
Related structure data | 7jgjMC 6xjaC 6xjbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22328.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | IgA1 Protease with mAb | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : murine mAb in complex with Streptoccocus pneumoniae IgA1 Protease
Entire | Name: murine mAb in complex with Streptoccocus pneumoniae IgA1 Protease |
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Components |
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-Supramolecule #1: murine mAb in complex with Streptoccocus pneumoniae IgA1 Protease
Supramolecule | Name: murine mAb in complex with Streptoccocus pneumoniae IgA1 Protease type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Immunoglobulin A1 protease
Supramolecule | Name: Immunoglobulin A1 protease / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: mAb
Supramolecule | Name: mAb / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Immunoglobulin A1 protease
Macromolecule | Name: Immunoglobulin A1 protease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
Molecular weight | Theoretical: 145.095812 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TEPEKKLELR NVSDIELYSQ TNGTYRQHVS LDGIPENTDT YFVKVKSSAF KDVYIPVASI TEEKRNGQSV YKITAKAEKL QQELENKYV DNFTFYLDKK AKEENTNFTS FSNLVKAINQ NPSGTYHLAA SLNANEVELG PDERSYIKDT FTGRLIGEKD G KNYAIYNL ...String: TEPEKKLELR NVSDIELYSQ TNGTYRQHVS LDGIPENTDT YFVKVKSSAF KDVYIPVASI TEEKRNGQSV YKITAKAEKL QQELENKYV DNFTFYLDKK AKEENTNFTS FSNLVKAINQ NPSGTYHLAA SLNANEVELG PDERSYIKDT FTGRLIGEKD G KNYAIYNL KKPLFENLSG ATVEKLSLKN VAISGKNDIG SLANEATNGT KIKQVHVDGV LAGERGVGGL LAKADQSSIA ES SFKGRIV NTYETTDAYN IGGLVGHLTG KNASIAKSKA TVTISSNTNR SDQTVGGLAG LVDQDAHIQN SYAEGDINNV KHF GKVAGV AGYLWDRTSG EEKHAGELTN VLSDVNVTNG NAITGYHYTG MKVANTFSSK ANRVFNVTLE KDEVVSKESF EERG TMLDA SQIVSKKAEI NPLTLPTVEP LSTSGKKDSD FSKIAHYQAN RALVYKNIEK LLPFYNKSTI VKYGNLVKEN SLLYQ KELL SAVMMKDDQV ITDIVSNKQT ANKLLLHYND HSSEKFDLKY QTDFANLAEY NLGNTGLLYT PNQFLYDRDS IVKEVL PEL QKLDYQSDAI RKTLGISPEV KLTELYLEDQ FSKTKQNLGD SLKKLLSADA GLASDNSVTR GYLVDKIKNN KEALLLG LT YLERWYNFNY GQVNVKDLVM YHPDFFGKGN TSPLDTLIEL GKSGFNNLLA KNNVDTYGIS LASQHGATDL FSTLEHYR K VFLPNTSNND WFKSETKAYI VEEKSTIEEV KTKQGLAGTK YSIGVYDRIT SATWKYRNMV LPLLTLPERS VFVISTMSS LGFGAYDRYR SSDHKAGKAL NDFVEENARE TAKRQRDHYD YWYRILDEQS REKLYRTILL YDAYKFGDDT TSGKATAEAK FDSSNPAMK NFFGPVGNKV VHNQHGAYAT GDGVYYMSYR MLDKDGAITY THEMTHDSDQ DIYLGGYGRR NGLGPEFFAK G LLQAPDQP SDATITINSI LKHSKSDSTE GSRLQVLDPT ERFQNAADLQ NYVHNMFDLI YMMEYLEGQS IVNKLSVYQK MA ALRKIEN KYVKDPADGN EVYATNVVKE LTEAEARNLN SFESLIDHNI LSAREYQSGD YERNGYYTIK LFAPIYSALS SEK GTPGDL MGRRIAYELL AAKGFKDGMV PYISNQYEED AKQQGQTINL YGKERGLVTD ELVLKKVFDG KYKTWAEFKT AMYQ ERVDQ FGNLKQVTFK DPTKPWPSYG TKTINNVDEL QALMDQAVLK DAEGPRWSNY DPEIDSAVHK LKRAIFKAYL DQTND FRSS IFENKK |
-Macromolecule #2: mAB Light Chain
Macromolecule | Name: mAB Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.270615 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EEVLTQSPAI MSASPGEKVT MTCSASSSVS YIHWYQQKSN TSPKLWIYAT SKLASGVPGR FSGSGSGNSY SLTISSMEAE DVATYYCFQ GSGYPFTFGS GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String: EEVLTQSPAI MSASPGEKVT MTCSASSSVS YIHWYQQKSN TSPKLWIYAT SKLASGVPGR FSGSGSGNSY SLTISSMEAE DVATYYCFQ GSGYPFTFGS GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC |
-Macromolecule #3: mAB Heavy Chain
Macromolecule | Name: mAB Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.212004 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLQQSGPE LEKPGASMKI SCKASGYSFT GYNMNWVKQS NGKSLEWIGS IDPYTGGSNY NQKFMGKATL TVDKSSSTAY MQLKSLTSE DSAVYYCATV VGRVYAMDYW GQGTSVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String: EVQLQQSGPE LEKPGASMKI SCKASGYSFT GYNMNWVKQS NGKSLEWIGS IDPYTGGSNY NQKFMGKATL TVDKSSSTAY MQLKSLTSE DSAVYYCATV VGRVYAMDYW GQGTSVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 20.0 millimolar / Component - Name: HEPES / Details: 20 mM HEPES, pH 7.4 150 mM NaCl |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 64968 |