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Yorodumi- EMDB-10799: Cryo-EM structure of a BcsB pentamer in the context of an assembl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10799 | ||||||||||||||||||
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Title | Cryo-EM structure of a BcsB pentamer in the context of an assembled Bcs macrocomplex | ||||||||||||||||||
Map data | composite map made from two experimental sharpened maps of the same sample data | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information cellulose biosynthetic process / UDP-glucose metabolic process / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||
Authors | Zouhir S / Krasteva PV | ||||||||||||||||||
Funding support | 5 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Architecture and regulation of an enterobacterial cellulose secretion system. Authors: Wiem Abidi / Samira Zouhir / Meryem Caleechurn / Stéphane Roche / Petya Violinova Krasteva / Abstract: Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c- ...Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c-di-GMP. The molecular understanding of system assembly and cellulose secretion has been largely limited to the crystallographic studies of a distantly homologous BcsAB synthase tandem and a low-resolution reconstruction of an assembled macrocomplex that encompasses most of the inner membrane and cytosolic subunits and features an atypical layered architecture. Here, we present cryo-EM structures of the assembled Bcs macrocomplex, as well as multiple crystallographic snapshots of regulatory Bcs subcomplexes. The structural and functional data uncover the mechanism of asymmetric secretion system assembly and periplasmic crown polymerization and reveal unexpected subunit stoichiometry, multisite c-di-GMP recognition, and ATP-dependent regulation. | ||||||||||||||||||
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_10799.map.gz | 215.5 MB | EMDB map data format | |
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Header (meta data) | emd-10799-v30.xml emd-10799.xml | 25.2 KB 25.2 KB | Display Display | EMDB header |
Images | emd_10799.png | 195.9 KB | ||
Others | emd_10799_additional_1.map.gz emd_10799_additional_2.map.gz emd_10799_additional_3.map.gz emd_10799_additional_4.map.gz | 215.5 MB 218.5 MB 126.4 MB 126.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10799 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10799 | HTTPS FTP |
-Validation report
Summary document | emd_10799_validation.pdf.gz | 233.5 KB | Display | EMDB validaton report |
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Full document | emd_10799_full_validation.pdf.gz | 232.6 KB | Display | |
Data in XML | emd_10799_validation.xml.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10799 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10799 | HTTPS FTP |
-Related structure data
Related structure data | 6yg8MC 6yarC 6yayC 6yb3C 6yb5C 6ybbC 6ybuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10799.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | composite map made from two experimental sharpened maps of the same sample data | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05248 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 2.9A locally refined and sharpened map used for...
File | emd_10799_additional_1.map | ||||||||||||
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Annotation | 2.9A locally refined and sharpened map used for the main composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.1A average resolution sharpened map used for the main composite map
File | emd_10799_additional_2.map | ||||||||||||
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Annotation | 3.1A average resolution sharpened map used for the main composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Non sharpened map
File | emd_10799_additional_3.map | ||||||||||||
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Annotation | Non sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Non sharpened map
File | emd_10799_additional_4.map | ||||||||||||
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Annotation | Non sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the ...
Entire | Name: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly |
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Components |
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-Supramolecule #1: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the ...
Supramolecule | Name: Co-expression of Bcs subunits R, Q, A, B, E, F and G lead to the purification of a membrane complex assembly type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: 1094 / Location in cell: periplasm |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pCDF-duet |
Molecular weight | Theoretical: 734 KDa |
-Supramolecule #2: Homopentameric assembly of the BcsB protein
Supramolecule | Name: Homopentameric assembly of the BcsB protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: 1094 / Location in cell: periplasm |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pCDF-duet |
-Macromolecule #1: Bacterial cellulose secretion regulator BcsB
Macromolecule | Name: Bacterial cellulose secretion regulator BcsB / type: protein_or_peptide / ID: 1 / Details: Bacterial cellulose synthesis subunit B / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: 1094 |
Molecular weight | Theoretical: 86.184383 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN ...String: MKRKLFWICA VAMGMSAFPS FMTQATPATQ PLINAEPAVA AQTEQNPQVG QVMPGVQGAD APVVAQNGPS RDVKLTFAQI APPPGSMVL RGINPNGSIE FGMRSDEVVT KAMLNLEYTP SPSLLPVQSQ LKVYLNDELM GVLPVTKEQL GKKTLAQMPI N PLFITDFN RVRLEFVGHY QDVCENPAST TLWLDVGRSS GLDLTYQTLN VKNDLSHFPV PFFDPRDNRT NTLPMVFAGA PD VGLQQAS AIVASWFGSR SGWRGQNFPV LYNQLPDRNA IVFATNDKRP DFLRDHPAVK APVIEMINHP QNPYVKLLVV FGR DDKDLL QAAKGIAQGN ILFRGESVVV NEVKPLLPRK PYDAPNWVRT DRPVTFGELK TYEEQLQSSG LEPAAINVSL NLPP DLYLM RSTGIDMDIN YRYTMPPVKD SSRMDISLNN QFLQSFNLSS KQEANRLLLR IPVLQGLLDG KTDVSIPALK LGATN QLRF DFEYMNPMPG GSVDNCITFQ PVQNHVVIGD DSTIDFSKYY HFIPMPDLRA FANAGFPFSR MADLSQTITV MPKAPN EAQ METLLNTVGF IGAQTGFPAI NLTVTDDGST IQGKDADIMI IGGIPDKLKD DKQIDLLVQA TESWVKTPMR QTPFPGI VP DESDRAAETR STLTSSGAMA AVIGFQSPYN DQRSVIALLA DSPRGYEMLN DAVNDSGKRA TMFGSVAVIR ESGINSLR V GDVYYVGHLP WFERLWYALA NHPILLAVLA AISVILLAWV LWRLLRIISR RRLNPDNE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 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: 2.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6yg8: |