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Yorodumi- PDB-8gl3: De novo design of monomeric helical bundles for pH-controlled mem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gl3 | |||||||||
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Title | De novo design of monomeric helical bundles for pH-controlled membrane lysis | |||||||||
Components | pRLB-519 | |||||||||
Keywords | DE NOVO PROTEIN / protein design / pH-responsive / membrane lysis | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Goldbach, N. / Bera, A.K. / Baker, D. / Kang, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci / Year: 2023 Title: De novo design of monomeric helical bundles for pH-controlled membrane lysis. Authors: Nicolas Goldbach / Issa Benna / Basile I M Wicky / Jacob T Croft / Lauren Carter / Asim K Bera / Hannah Nguyen / Alex Kang / Banumathi Sankaran / Erin C Yang / Kelly K Lee / David Baker / Abstract: Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane ...Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gl3.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gl3.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gl3_validation.pdf.gz | 400.3 KB | Display | wwPDB validaton report |
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Full document | 8gl3_full_validation.pdf.gz | 401.8 KB | Display | |
Data in XML | 8gl3_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 8gl3_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/8gl3 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8gl3 | HTTPS FTP |
-Related 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: 27599.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Sodium fluoride and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.64 Å / Num. obs: 11502 / % possible obs: 98.36 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.052 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 7.39 / Num. unique obs: 2812 / CC1/2: 0.976 / Rpim(I) all: 0.091 / % possible all: 98.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.64 Å / SU ML: 0.2172 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.0929 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.04 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.64 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.879 Å / Origin y: -7.312 Å / Origin z: 36.152 Å
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Refinement TLS group | Selection details: ( CHAIN A AND RESID 6:221 ) |