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Yorodumi- EMDB-30923: CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30923 | |||||||||
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Title | CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (MceA) complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MceA / Microcin E492 / Bacteriocin / PTS / ManYZ / transporter / Mannose / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information N-acetylglucosamine transport / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / monoatomic ion transmembrane transport / killing of cells of another organism / defense response to bacterium ...N-acetylglucosamine transport / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / monoatomic ion transmembrane transport / killing of cells of another organism / defense response to bacterium / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) / Klebsiella pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.28 Å | |||||||||
Authors | Wang JW / Zeng JW | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the mannose phosphotransferase system (man-PTS) complexed with microcin E492, a pore-forming bacteriocin. Authors: Kai Huang / Jianwei Zeng / Xueli Liu / Tianyu Jiang / Jiawei Wang / | |||||||||
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_30923.map.gz | 14 MB | EMDB map data format | |
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Header (meta data) | emd-30923-v30.xml emd-30923.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30923_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_30923.png | 67.2 KB | ||
Filedesc metadata | emd-30923.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30923 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30923 | HTTPS FTP |
-Validation report
Summary document | emd_30923_validation.pdf.gz | 359.5 KB | Display | EMDB validaton report |
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Full document | emd_30923_full_validation.pdf.gz | 359 KB | Display | |
Data in XML | emd_30923_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_30923_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30923 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30923 | HTTPS FTP |
-Related structure data
Related structure data | 7dyrMC 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_30923.map.gz / Format: CCP4 / Size: 244.1 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: 1.061 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 : ManYZ trimer complex with Microcin E492 (MceA)
Entire | Name: ManYZ trimer complex with Microcin E492 (MceA) |
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Components |
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-Supramolecule #1: ManYZ trimer complex with Microcin E492 (MceA)
Supramolecule | Name: ManYZ trimer complex with Microcin E492 (MceA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Molecular weight | Theoretical: 0.53 kDa/nm |
-Macromolecule #1: PTS system mannose-specific EIIC component
Macromolecule | Name: PTS system mannose-specific EIIC component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 27.647621 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ ...String: MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ NMLNAIPEVV TNGLNIAGGM IVVVGYAMVI NMMRAGYLMP FFYLGFVTAA FTNFNLVALG VIGTVMAVLY IQ LSPKYNR VAGAPAQAAG NNDLDNELD UniProtKB: PTS system mannose-specific EIIC component |
-Macromolecule #2: PTS system mannose-specific EIID component
Macromolecule | Name: PTS system mannose-specific EIID component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 30.983373 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY ...String: MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY GYSKGIDIVK DMGGGFLQKL TEGASILGLF VMGALVNKWT HVNIPLVVSR ITDQTGKEHV TTVQTILDQL MP GLVPLLL TFACMWLLRK KVNPLWIIVG FFVIGIAGYA CGLLGL UniProtKB: PTS system mannose-specific EIID component |
-Macromolecule #3: Microcin E492
Macromolecule | Name: Microcin E492 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella pneumoniae (bacteria) |
Molecular weight | Theoretical: 7.887492 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: GETDPNTQLL NDLGNNMAWG AALGAPGGLG SAALGAAGGA LQTVGQGLID HGPVNVPIPV LIGPSWNGSG SGYNSATSSS GSGS UniProtKB: Microcin E492 |
-Macromolecule #4: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |