+Open data
-Basic information
Entry | Database: PDB / ID: 6k1h | ||||||||||||
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Title | Structure of membrane protein | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / PTS / ManYZ / transporter / Mannose | ||||||||||||
Function / homology | Function and homology information mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||
Authors | Wang, J.W. / Zeng, J.W. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell Res / Year: 2019 Title: Structure of the mannose transporter of the bacterial phosphotransferase system. Authors: Xueli Liu / Jianwei Zeng / Kai Huang / Jiawei Wang / | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6k1h.cif.gz | 264 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k1h.ent.gz | 214.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k1h_validation.pdf.gz | 997.2 KB | Display | wwPDB validaton report |
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Full document | 6k1h_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6k1h_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 6k1h_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1h ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1h | HTTPS FTP |
-Related structure data
Related structure data | 9906MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 30983.373 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: D8B36_09735 / Variant: K-12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): BL21 / References: UniProt: A0A387CW08, UniProt: P69805*PLUS #2: Protein | Mass: 28752.783 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: manY, pel, ptsP, b1818, JW1807 / Variant: K-12 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Variant (production host): BL21 / References: UniProt: P69801 #3: Sugar | Has ligand of interest | Y | |
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-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: ManYZ trimer complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 176 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain: BL21 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309996 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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