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- PDB-6xs8: Crystal structure of Chaetomium thermophilum Vps29 complexed with... -

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Basic information

Entry
Database: PDB / ID: 6xs8
TitleCrystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3
Components
  • 48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsPROTEIN TRANSPORT/INHIBITOR / Vps29 / Retromer / Endosome / Protein transport / cyclic peptide / inhibitor / PROTEIN TRANSPORT-INHIBITOR complex
Function / homology
Function and homology information


retromer complex / retrograde transport, endosome to Golgi / protein transport / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95009854987 Å
AuthorsChen, K.-E. / Guo, Q. / Collins, B.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101743 Australia
CitationJournal: 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
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 29
B: 48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA


Theoretical massNumber of molelcules
Total (without water)23,9552
Polymers23,9552
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, ctVps29 maintained the monomeric state in the presence of RT-D3.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.520, 47.520, 170.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21B-105-

HOH

31B-107-

HOH

41B-109-

HOH

51B-110-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole


Mass: 22387.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RZB5
#2: Protein/peptide 48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA


Mass: 1567.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cyclic peptide RT-D3 / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.18 M ammonium citrate dibasic and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→42.75 Å / Num. obs: 20527 / % possible obs: 99.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 16.885 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.013 / Rrim(I) all: 0.041 / Net I/σ(I): 28 / Num. measured all: 209530 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.8710.50.1461261612060.9950.0470.1549.599
8.97-42.755.80.0289771690.9990.0120.03136.373.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.83 Å41.15 Å
Translation1.83 Å41.15 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.5.6phasing
PHENIX1.10.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W8M

5w8m


Resolution: 1.95009854987→41.1509291116 Å / SU ML: 0.199634091036 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.266463367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251255925476 872 5.14697202219 %
Rwork0.204687714451 16070 -
obs0.20705055269 16942 98.6721025044 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.446980057 Å2
Refinement stepCycle: LAST / Resolution: 1.95009854987→41.1509291116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 166 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114802103171630
X-RAY DIFFRACTIONf_angle_d1.314434894232216
X-RAY DIFFRACTIONf_chiral_restr0.0736810685054256
X-RAY DIFFRACTIONf_plane_restr0.00813673023727282
X-RAY DIFFRACTIONf_dihedral_angle_d21.431754629613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.07230.2667132080141520.2204568985852597X-RAY DIFFRACTION98.2487491065
2.0723-2.23230.2379798566961160.2159063834872634X-RAY DIFFRACTION98.7787356322
2.2323-2.45690.3229774577671750.2510619941432600X-RAY DIFFRACTION98.9304812834
2.4569-2.81230.2445571468751310.20526453182727X-RAY DIFFRACTION99.9650227352
2.8123-3.54290.2743609345951420.1913562694942727X-RAY DIFFRACTION99.9651567944
3.5429-41.15090.2047026129481560.1867136833452785X-RAY DIFFRACTION96.2999345121

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