+Open data
-Basic information
Entry | Database: PDB / ID: 6lar | ||||||
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Title | Structure of ESX-3 complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wang, S.H. / Zhou, K.X. / Li, J. / Rao, Z.H. | ||||||
Citation | Journal: To Be Published Title: cryo-em structure of esx-3 Authors: Wang, S.H. / Zhou, K.X. / Li, J. / Rao, Z.H. | ||||||
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 | 6lar.cif.gz | 513.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lar.ent.gz | 409.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lar_validation.pdf.gz | 862.7 KB | Display | wwPDB validaton report |
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Full document | 6lar_full_validation.pdf.gz | 943.5 KB | Display | |
Data in XML | 6lar_validation.xml.gz | 87.1 KB | Display | |
Data in CIF | 6lar_validation.cif.gz | 132.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6lar ftp://data.pdbj.org/pub/pdb/validation_reports/la/6lar | HTTPS FTP |
-Related structure data
Related structure data | 0862MC 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: 53684.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: eccB3 / Production host: Escherichia coli (E. coli) References: UniProt: A0QQ39, Hydrolases; Acting on acid anhydrides #2: Protein | Mass: 48292.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: eccD3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ46 #3: Protein | Mass: 49900.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: eccC3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ40 #4: Protein | Mass: 33226.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: eccE3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QQ48 |
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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: esx-3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
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: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal magnification: 29000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4823 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215839 / Symmetry type: POINT |