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Yorodumi- PDB-6xs5: Crystal structure of human Vps29 complexed with RaPID-derived cyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xs5 | ||||||
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Title | Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/INHIBITOR / Vps29 / Retromer / Endosome / Protein transport / cyclic peptide / inhibitor / PROTEIN TRANSPORT-INHIBITOR complex | ||||||
Function / homology | Function and homology information retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Chen, K.-E. / Guo, Q. / Collins, B.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Authors: Kai-En Chen / Qian Guo / Timothy A Hill / Yi Cui / Amy K Kendall / Zhe Yang / Ryan J Hall / Michael D Healy / Joanna Sacharz / Suzanne J Norwood / Sachini Fonseka / Boyang Xie / Robert C ...Authors: Kai-En Chen / Qian Guo / Timothy A Hill / Yi Cui / Amy K Kendall / Zhe Yang / Ryan J Hall / Michael D Healy / Joanna Sacharz / Suzanne J Norwood / Sachini Fonseka / Boyang Xie / Robert C Reid / Natalya Leneva / Robert G Parton / Rajesh Ghai / David A Stroud / David P Fairlie / Hiroaki Suga / Lauren P Jackson / Rohan D Teasdale / Toby Passioura / Brett M Collins / Abstract: The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and ...The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xs5.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xs5.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xs5 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xs5 | HTTPS FTP |
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-Related structure data
Related structure data | 6xs7C 6xs8C 6xs9C 6xsaC 1w24S 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: 21636.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Plasmid: pGEX-4T2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBQ0 | ||||||
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#2: Protein/peptide | Mass: 1984.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cyclic peptide RT-D1 derived from RaPID screen / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | #4: Chemical | ChemComp-FMT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.5 M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953729 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→42.41 Å / Num. obs: 14169 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.373 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1030 / CC1/2: 0.917 / Rpim(I) all: 0.235 / Rrim(I) all: 0.632 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W24 Resolution: 2.01→42.41 Å / SU ML: 0.205837110947 / Cross valid method: FREE R-VALUE / σ(F): 1.37769675716 / Phase error: 25.274220866 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 32.3112114153 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→42.41 Å
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Refine LS restraints |
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LS refinement shell |
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