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Yorodumi- PDB-7w6y: Crystal structure of Kangiella koreensis RseP orthologue in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w6y | |||||||||||||||
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Title | Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P1 | |||||||||||||||
Components | Anti sigma-E protein, RseA | |||||||||||||||
Keywords | HYDROLASE / Intramembrane protease | |||||||||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Kangiella koreensis DSM 16069 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | |||||||||||||||
Authors | Imaizumi, Y. / Takanuki, K. / Nogi, T. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Sci Adv / Year: 2022 Title: Mechanistic insights into intramembrane proteolysis by site-2 protease homolog RseP. Authors: Yuki Imaizumi / Kazunori Takanuki / Takuya Miyake / Mizuki Takemoto / Kunio Hirata / Mika Hirose / Rika Oi / Tatsuya Kobayashi / Kenichi Miyoshi / Rie Aruga / Tatsuhiko Yokoyama / Shizuka ...Authors: Yuki Imaizumi / Kazunori Takanuki / Takuya Miyake / Mizuki Takemoto / Kunio Hirata / Mika Hirose / Rika Oi / Tatsuya Kobayashi / Kenichi Miyoshi / Rie Aruga / Tatsuhiko Yokoyama / Shizuka Katagiri / Hiroaki Matsuura / Kenji Iwasaki / Takayuki Kato / Mika K Kaneko / Yukinari Kato / Michiko Tajiri / Satoko Akashi / Osamu Nureki / Yohei Hizukuri / Yoshinori Akiyama / Terukazu Nogi / Abstract: Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal ...Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w6y.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w6y.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 7w6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w6y_validation.pdf.gz | 720.3 KB | Display | wwPDB validaton report |
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Full document | 7w6y_full_validation.pdf.gz | 725.4 KB | Display | |
Data in XML | 7w6y_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7w6y_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6y ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6y | HTTPS FTP |
-Related structure data
Related structure data | 7w6xC 7w6zC 7w70C 7w71C 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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Unit cell |
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-Components
#1: Protein | Mass: 50443.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kangiella koreensis DSM 16069 (bacteria) Strain: DSM 16069 / KCTC 12182 / SW-125 / Gene: Kkor_0748 / Production host: Escherichia coli (E. coli) / References: UniProt: C7R5Z1 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-BAT / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.24 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 28-30% (vol./vol.) Polyethylene glycol 500 monomethyl ether, 100 mM NaCl, 100 mM CaCl2, and 100 mM HEPES-Na (pH7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.3 Å / Num. obs: 22986 / % possible obs: 99.8 % / Redundancy: 135.8 % / Biso Wilson estimate: 97.24 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 20 |
Reflection shell | Resolution: 3.1→3.21 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1130 / CC1/2: 0.821 / Rpim(I) all: 1.601 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.1→40.91 Å / SU ML: 0.5177 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.5898 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→40.91 Å
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Refine LS restraints |
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LS refinement shell |
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