+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45192 | |||||||||||||||
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Title | Cryo-EM structure of PqqU with ligand PQQ | |||||||||||||||
Map data | Cryo-EM structure of E. coli PqqU with ligand PQQ at 1.99 A global resolution. | |||||||||||||||
Sample |
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Keywords | TonD-dependent / outer membrane / transporter / PQQ uptake / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / intracellular monoatomic cation homeostasis / transmembrane transporter complex / cell outer membrane / signaling receptor activity / membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli BW25113 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.99 Å | |||||||||||||||
Authors | Munder F / Venugopal H / Grinter R | |||||||||||||||
Funding support | Australia, 4 items
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Citation | Journal: To Be Published Title: High-affinity PQQ import is widespread in Gram-negative bacteria. Authors: Munder F / Voutsinos M / Hantke K / Venugopal H / Grinter R | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45192.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-45192-v30.xml emd-45192.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45192_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_45192.png | 189.4 KB | ||
Filedesc metadata | emd-45192.cif.gz | 6.4 KB | ||
Others | emd_45192_half_map_1.map.gz emd_45192_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45192 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45192 | HTTPS FTP |
-Validation report
Summary document | emd_45192_validation.pdf.gz | 943.1 KB | Display | EMDB validaton report |
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Full document | emd_45192_full_validation.pdf.gz | 942.7 KB | Display | |
Data in XML | emd_45192_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_45192_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45192 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45192 | HTTPS FTP |
-Related structure data
Related structure data | 9c4oMC 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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-Map
File | Download / File: emd_45192.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of E. coli PqqU with ligand PQQ at 1.99 A global resolution. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map B of PqqU with ligand PQQ.
File | emd_45192_half_map_1.map | ||||||||||||
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Annotation | Half Map B of PqqU with ligand PQQ. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A of PqqU with ligand PQQ.
File | emd_45192_half_map_2.map | ||||||||||||
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Annotation | Half Map A of PqqU with ligand PQQ. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of PqqU with PQQ
Entire | Name: Complex of PqqU with PQQ |
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Components |
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-Supramolecule #1: Complex of PqqU with PQQ
Supramolecule | Name: Complex of PqqU with PQQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: TonB-dependent outer membrane transporter PqqU in complex with its substrate PQQ. |
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Source (natural) | Organism: Escherichia coli BW25113 (bacteria) |
Molecular weight | Theoretical: 78 KDa |
-Macromolecule #1: Pyrroloquinoline quinone transporter
Macromolecule | Name: Pyrroloquinoline quinone transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BW25113 (bacteria) |
Molecular weight | Theoretical: 78.401164 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSNHHHHHHH HHHENLYFQG AMDIGINSDP ADEQTMIVSA APQVVSELDT PAAVSVVDGE EMRLATPRIN LSESLTGVPG LQVQNRQNY AQDLQLSIRG FGSRSTYGIR GIRLYVDGIP ATMPDGQGQT SNIDLSSVQN VEVLRGPFSA LYGNASGGVM N VTTQTGQQ ...String: MSNHHHHHHH HHHENLYFQG AMDIGINSDP ADEQTMIVSA APQVVSELDT PAAVSVVDGE EMRLATPRIN LSESLTGVPG LQVQNRQNY AQDLQLSIRG FGSRSTYGIR GIRLYVDGIP ATMPDGQGQT SNIDLSSVQN VEVLRGPFSA LYGNASGGVM N VTTQTGQQ PPTIEASSYY GSFGSWRYGL KATGATGDGT QPGDVDYTVS TTRFTTHGYR DHSGAQKNLA NAKLGVRIDE AS KLSLIFN SVDIKADDPG GLTKAEWKAN PQQAPRAEQY DTRKTIKQTQ AGLRYERSLS SRDDMSVMMY AGERETTQYQ SIP MAPQLN PSHAGGVITL QRHYQGIDSR WTHRGELGVP VTFTTGLNYE NMSENRKGYN NFRLNSGMPE YGQKGELRRD ERNL MWNID PYLQTQWQLS EKLSLDAGVR YSSVWFDSND HYVTPGNGDD SGDASYHKWL PAGSLKYAMT DAWNIYLAAG RGFET PTIN ELSYRADGQS GMNLGLKPST NDTIEIGSKT RIGDGLLSLA LFQTDTDDEI VVDSSSGGRT TYKNAGKTRR QGAELA WDQ RFAGDFRVNA SWTWLDATYR SNVCNEQDCN GNRMPGIARN MGFASIGYVP EDGWYAGTEA RYMGDIMADD ENTAKAP SY TLVGLFTGYK YNYHNLTVDL FGRVDNLFDK EYVGSVIVNE SNGRYYEPSP GRNYGVGMNI AWRFE UniProtKB: Pyrroloquinoline quinone transporter |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: PYRROLOQUINOLINE QUINONE
Macromolecule | Name: PYRROLOQUINOLINE QUINONE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PQQ |
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Molecular weight | Theoretical: 330.206 Da |
Chemical component information | ChemComp-PQQ: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 111 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: LMNG was partly removed by concentration in a 100 kDa cut-off concentrator. | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 microliters of sample. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 8744 / Average exposure time: 5.22 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |