+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34668 | |||||||||
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Title | Cell divisome sPG hydrolysis machinery FtsEX-EnvC | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacterial cell divison / divisome PG hydrolysis / ABC transporter / Regulator / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / extrinsic component of membrane ...division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / extrinsic component of membrane / cell division site / ATPase complex / positive regulation of cell division / transmembrane transporter activity / response to radiation / transmembrane transport / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / cell division / response to antibiotic / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Zhang Z / Chen Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Structural insight into the septal peptidoglycan hydrolysis machinery of bacterial cell division Authors: Zhang Z / Dong H / Chen Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34668.map.gz | 685 MB | EMDB map data format | |
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Header (meta data) | emd-34668-v30.xml emd-34668.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34668_fsc.xml | 19 KB | Display | FSC data file |
Images | emd_34668.png | 43.5 KB | ||
Masks | emd_34668_msk_1.map | 729 MB | Mask map | |
Filedesc metadata | emd-34668.cif.gz | 6.1 KB | ||
Others | emd_34668_half_map_1.map.gz emd_34668_half_map_2.map.gz | 677.2 MB 677.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34668 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34668 | HTTPS FTP |
-Validation report
Summary document | emd_34668_validation.pdf.gz | 709.5 KB | Display | EMDB validaton report |
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Full document | emd_34668_full_validation.pdf.gz | 709.1 KB | Display | |
Data in XML | emd_34668_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | emd_34668_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34668 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34668 | HTTPS FTP |
-Related structure data
Related structure data | 8hd0MC 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_34668.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34668_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34668_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34668_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC
Entire | Name: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC |
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Components |
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-Supramolecule #1: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC
Supramolecule | Name: Bacterial divisom sPG hydrolysis machinery FtsEX-EnvC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Bacterial cell division septal peptidoglycon hydrolysis mechinary complex FtsEX=EnvC |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MG1655 |
Molecular weight | Theoretical: 126 KDa |
-Macromolecule #1: Cell division ATP-binding protein FtsE
Macromolecule | Name: Cell division ATP-binding protein FtsE / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 24.475295 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MIRFEHVSKA YLGGRQALQG VTFHMQPGEM AFLTGHSGAG KSTLLKLICG IERPSAGKIW FSGHDITRLK NREVPFLRRQ IGMIFQDHH LLMDRTVYDN VAIPLIIAGA SGDDIRRRVS AALDKVGLLD KAKNFPIQLS GGEQQRVGIA RAVVNKPAVL L ADQPTGNL ...String: MIRFEHVSKA YLGGRQALQG VTFHMQPGEM AFLTGHSGAG KSTLLKLICG IERPSAGKIW FSGHDITRLK NREVPFLRRQ IGMIFQDHH LLMDRTVYDN VAIPLIIAGA SGDDIRRRVS AALDKVGLLD KAKNFPIQLS GGEQQRVGIA RAVVNKPAVL L ADQPTGNL DDALSEGILR LFEEFNRVGV TVLMATHDIN LISRRSYRML TLSDGHLHGG VGHE UniProtKB: Cell division ATP-binding protein FtsE |
-Macromolecule #2: Cell division protein FtsX
Macromolecule | Name: Cell division protein FtsX / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 38.5835 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN ...String: MNKRDAINHI RQFGGRLDRF RKSVGGSGDG GRNAPKRAKS SPKPVNRKTN VFNEQVRYAF HGALQDLKSK PFATFLTVMV IAISLTLPS VCYMVYKNVN QAATQYYPSP QITVYLQKTL DDDAAAGVVA QLQAEQGVEK VNYLSREDAL GEFRNWSGFG G ALDMLEEN PLPAVAVVIP KLDFQGTESL NTLRDRITQI NGIDEVRMDD SWFARLAALT GLVGRVSAMI GVLMVAAVFL VI GNSVRLS IFARRDSINV QKLIGATDGF ILRPFLYGGA LLGFSGALLS LILSEILVLR LSSAVAEVAQ VFGTKFDING LSF DECLLL LLVCSMIGWV AAWLATVQHL RHFTPE UniProtKB: Cell division protein FtsX |
-Macromolecule #3: Murein hydrolase activator EnvC
Macromolecule | Name: Murein hydrolase activator EnvC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 46.661617 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MTRAVKPRRF AIRPIIYASV LSAGVLLCAF SAHADERDQL KSIQADIAAK ERAVRQKQQQ RASLLAQLKK QEEAISEATR KLRETQNTL NQLNKQIDEM NASIAKLEQQ KAAQERSLAA QLDAAFRQGE HTGIQLILSG EESQRGQRLQ AYFGYLNQAR Q ETIAQLKQ ...String: MTRAVKPRRF AIRPIIYASV LSAGVLLCAF SAHADERDQL KSIQADIAAK ERAVRQKQQQ RASLLAQLKK QEEAISEATR KLRETQNTL NQLNKQIDEM NASIAKLEQQ KAAQERSLAA QLDAAFRQGE HTGIQLILSG EESQRGQRLQ AYFGYLNQAR Q ETIAQLKQ TREEVAMQRA ELEEKQSEQQ TLLYEQRAQQ AKLTQALNER KKTLAGLESS IQQGQQQLSE LRANESRLRN SI ARAEAAA KARAEREARE AQAVRDRQKE ATRKGTTYKP TESEKSLMSR TGGLGAPRGQ AFWPVRGPTL HRYGEQLQGE LRW KGMVIG ASEGTEVKAI ADGRVILADW LQGYGLVVVV EHGKGDMSLY GYNQSALVSV GSQVRAGQPI ALVGSSGGQG RPSL YFEIR RQGQAVNPQP WLGR UniProtKB: Murein hydrolase activator EnvC |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8hd0: |