+Open data
-Basic information
Entry | Database: PDB / ID: 9c4o | |||||||||||||||
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Title | Cryo-EM structure of PqqU with ligand PQQ | |||||||||||||||
Components | Pyrroloquinoline quinone transporter | |||||||||||||||
Keywords | MEMBRANE PROTEIN / TonD-dependent / outer membrane / transporter / PQQ uptake | |||||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å | |||||||||||||||
Authors | Munder, F. / Venugopal, H. / Grinter, R. | |||||||||||||||
Funding support | Australia, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c4o.cif.gz | 248.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c4o.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 9c4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c4o_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9c4o_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9c4o_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 9c4o_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/9c4o ftp://data.pdbj.org/pub/pdb/validation_reports/c4/9c4o | HTTPS FTP |
-Related structure data
Related structure data | 45192MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 78401.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: pqqU, yncD, b1451, JW1446 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76115 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-PQQ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of PqqU with PQQ / Type: COMPLEX Details: TonB-dependent outer membrane transporter PqqU in complex with its substrate PQQ. Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.078 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli BW25113 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.4 Details: LMNG was partly removed by concentration in a 100 kDa cut-off concentrator. | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 3 microliters of sample |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.22 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 8744 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2110000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 872884 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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