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Yorodumi- PDB-7cu8: Crystal structure of the soluble domain of TiME protein from Myco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cu8 | ||||||
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Title | Crystal structure of the soluble domain of TiME protein from Mycobacterium tuberculosis | ||||||
Components | Tube-forming protein in Mycobacterial Envelope (TiME) | ||||||
Keywords | PROTEIN TRANSPORT / tubular protein / envelope-spanning channel / potential drug target | ||||||
Function / homology | PknH-like extracellular domain / PknH-like extracellular domain superfamily / PknH-like extracellular domain / Conserved protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Gong, W. / Cai, X. / Liu, L. / Wen, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: Identification and architecture of a putative secretion tube across mycobacterial outer envelope. Authors: Xiaoying Cai / Lei Liu / Chunhong Qiu / Chongzheng Wen / Yao He / Yanxiang Cui / Siyu Li / Xuan Zhang / Longhua Zhang / Changlin Tian / Lijun Bi / Z Hong Zhou / Weimin Gong / Abstract: Tuberculosis-causing mycobacteria have thick cell-wall and capsule layers that are formed from complex structures. Protein secretion across these barriers depends on a specialized protein secretion ...Tuberculosis-causing mycobacteria have thick cell-wall and capsule layers that are formed from complex structures. Protein secretion across these barriers depends on a specialized protein secretion system, but none has been reported. We show that Rv3705c and its homologous MSMEG_6251 in are tube-forming proteins in the mycobacterial envelope (TiME). Crystallographic and cryo-EM structures of these two proteins show that both proteins form rotationally symmetric rings. Two layers of TiME rings pack together in a tail-to-tail manner into a ring-shaped complex, which, in turn, stacks together to form tubes. TiME was detected mainly in the cell wall and capsule. Knocking out the TiME gene markedly decreased the amount of secreted protein in the culture medium, and expression of this gene in knocked-out strain partially restored the level of secreted protein. Our structure and functional data thus suggest that TiME forms a protein transport tube across the mycobacterial outer envelope. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cu8.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cu8.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 7cu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cu8_validation.pdf.gz | 485.7 KB | Display | wwPDB validaton report |
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Full document | 7cu8_full_validation.pdf.gz | 487.6 KB | Display | |
Data in XML | 7cu8_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 7cu8_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/7cu8 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/7cu8 | HTTPS FTP |
-Related structure data
Related structure data | 7cu9SC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 21536.834 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: Rv3705c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6XI06 #2: Chemical | ChemComp-SO4 / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.83 Å3/Da / Density % sol: 82 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.2M lithium sulfate monohydrate, 0.1M Tris pH 8.8, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 64048 / % possible obs: 99.8 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 72.3 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.142 / Num. unique obs: 6276 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CU9 Resolution: 3.3→49.78 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.874 / SU B: 13.338 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.41 Å2 / Biso mean: 54.969 Å2 / Biso min: 38.18 Å2
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Refinement step | Cycle: final / Resolution: 3.3→49.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.383 Å / Rfactor Rfree error: 0
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