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Yorodumi- EMDB-22843: Cryo-electron microscopy structure of the heavy metal efflux pump... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22843 | |||||||||
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Title | Cryo-electron microscopy structure of the heavy metal efflux pump CusA in the symmetric closed state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | efflux / pump / heavy metal. copper / silver / closed / open / transport / MEMBRANE PROTEIN / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information silver ion transmembrane transporter activity / silver ion transport / plasma membrane copper ion transport / silver ion transmembrane transport / copper ion transmembrane transport / response to silver ion / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion ...silver ion transmembrane transporter activity / silver ion transport / plasma membrane copper ion transport / silver ion transmembrane transport / copper ion transmembrane transport / response to silver ion / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / intracellular copper ion homeostasis / response to toxic substance / copper ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Moseng MA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: mBio / Year: 2021 Title: Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion Export. Authors: Mitchell A Moseng / Meinan Lyu / Tanadet Pipatpolkai / Przemyslaw Glaza / Corey C Emerson / Phoebe L Stewart / Phillip J Stansfeld / Edward W Yu / Abstract: Gram-negative bacteria utilize the resistance-nodulation-cell division (RND) superfamily of efflux pumps to expel a variety of toxic compounds from the cell. The CusA membrane protein, which ...Gram-negative bacteria utilize the resistance-nodulation-cell division (RND) superfamily of efflux pumps to expel a variety of toxic compounds from the cell. The CusA membrane protein, which recognizes and extrudes biocidal Cu(I) and Ag(I) ions, belongs to the heavy-metal efflux (HME) subfamily of RND efflux pumps. We here report four structures of the trimeric CusA heavy-metal efflux pump in the presence of Cu(I) using single-particle cryo-electron microscopy (cryo-EM). We discover that different CusA protomers within the trimer are able to bind Cu(I) ions simultaneously. Our structural data combined with molecular dynamics (MD) simulations allow us to propose a mechanism for ion transport where each CusA protomer functions independently within the trimer. The bacterial RND superfamily of efflux pumps mediate resistance to a variety of biocides, including Cu(I) and Ag(I) ions. Here we report four cryo-EM structures of the trimeric CusA pump in the presence of Cu(I). Combined with MD simulations, our data indicate that each CusA protomer within the trimer recognizes and extrudes Cu(I) independently. | |||||||||
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_22843.map.gz | 13 MB | EMDB map data format | |
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Header (meta data) | emd-22843-v30.xml emd-22843.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_22843.png | 210.4 KB | ||
Filedesc metadata | emd-22843.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22843 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22843 | HTTPS FTP |
-Validation report
Summary document | emd_22843_validation.pdf.gz | 516.8 KB | Display | EMDB validaton report |
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Full document | emd_22843_full_validation.pdf.gz | 516.3 KB | Display | |
Data in XML | emd_22843_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_22843_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22843 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22843 | HTTPS FTP |
-Related structure data
Related structure data | 7kf5MC 7kf6C 7kf7C 7kf8C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22843.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 : CusA in symmetric closed extrusion form
Entire | Name: CusA in symmetric closed extrusion form |
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Components |
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-Supramolecule #1: CusA in symmetric closed extrusion form
Supramolecule | Name: CusA in symmetric closed extrusion form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Cation efflux system protein CusA
Macromolecule | Name: Cation efflux system protein CusA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 115.833945 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHHHHHHMI EWIIRRSVAN RFLVLMGALF LSIWGTWTII NTPVDALPDL SDVQVIIKTS YPGQAPQIVE NQVTYPLTTT MLSVPGAKT VRGFSQFGDS YVYVIFEDGT DPYWARSRVL EYLNQVQGKL PAGVSAELGP DATGVGWIYE YALVDRSGKH D LADLRSLQ ...String: MGHHHHHHMI EWIIRRSVAN RFLVLMGALF LSIWGTWTII NTPVDALPDL SDVQVIIKTS YPGQAPQIVE NQVTYPLTTT MLSVPGAKT VRGFSQFGDS YVYVIFEDGT DPYWARSRVL EYLNQVQGKL PAGVSAELGP DATGVGWIYE YALVDRSGKH D LADLRSLQ DWFLKYELKT IPDVAEVASV GGVVKEYQVV IDPQRLAQYG ISLAEVKSAL DASNQEAGGS SIELAEAEYM VR ASGYLQT LDDFNHIVLK ASENGVPVYL RDVAKVQIGP EMRRGIAELN GEGEVAGGVV ILRSGKNARE VIAAVKDKLE TLK SSLPEG VEIVTTYDRS QLIDRAIDNL SGKLLEEFIV VAVVCALFLW HVRSALVAII SLPLGLCIAF IVMHFQGLNA NIMS LGGIA IAVGAMVDAA IVMIENAHKR LEEWQHQHPD ATLDNKTRWQ VITDASVEVG PALFISLLII TLSFIPIFTL EGQEG RLFG PLAFTKTYAM AGAALLAIVV IPILMGYWIR GKIPPESSNP LNRFLIRVYH PLLLKVLHWP KTTLLVAALS VLTVLW PLN KVGGEFLPQI NEGDLLYMPS TLPGISAAEA ASMLQKTDKL IMSVPEVARV FGKTGKAETA TDSAPLEMVE TTIQLKP QE QWRPGMTMDK IIEELDNTVR LPGLANLWVP PIRNRIDMLS TGIKSPIGIK VSGTVLADID AMAEQIEEVA RTVPGVAS A LAERLEGGRY INVEINREKA ARYGMTVADV QLFVTSAVGG AMVGETVEGI ARYPINLRYP QSWRDSPQAL RQLPILTPM KQQITLADVA DIKVSTGPSM LKTENARPTS WIYIDARDRD MVSVVHDLQK AIAEKVQLKP GTSVAFSGQF ELLERANHKL KLMVPMTLM IIFVLLYLAF RRVGEALLII SSVPFALVGG IWLLWWMGFH LSVATGTGFI ALAGVAAEFG VVMLMYLRHA I EAVPSLNN PQTFSEQKLD EALYHGAVLR VRPKAMTVAV IIAGLLPILW GTGAGSEVMS RIAAPMIGGM ITAPLLSLFI IP AAYKLMW LHRHRVRK UniProtKB: Cation efflux system protein CusA |
-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 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13304 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |