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- PDB-9o9i: Crystal structure of mouse Vps29 bound to DENND4C peptide (re-ref... -

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Basic information

Entry
Database: PDB / ID: 9o9i
TitleCrystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)
Components
  • ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU
  • Isoform 2 of Vacuolar protein sorting-associated protein 29
KeywordsPROTEIN TRANSPORT / Retromer / endosome / membrane trafficking / DENN domain
Function / homology
Function and homology information


regulation of Rab protein signal transduction / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / insulin-responsive compartment / retromer complex / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / retrograde transport, endosome to Golgi / cytoplasmic vesicle membrane ...regulation of Rab protein signal transduction / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / insulin-responsive compartment / retromer complex / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / retrograde transport, endosome to Golgi / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / cellular response to insulin stimulus / protein transport / cytoplasmic vesicle / endosome membrane / intracellular membrane-bounded organelle / Golgi apparatus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
: / dDENN domain / uDENN domain / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN ...: / dDENN domain / uDENN domain / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN / Domain always found downstream of DENN domain, found in a variety of signalling proteins / MABP domain / Tripartite DENN domain / Tripartite DENN domain profile. / MABP domain profile. / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / DENN domain-containing protein 4C / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, K.-E. / Collins, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2016410 Australia
Australian Research Council (ARC) Australia
CitationJournal: Nat Commun / Year: 2025
Title: Mapping of endosomal proximity proteomes reveals Retromer as a hub for RAB GTPase regulation.
Authors: Anton-Plagaro, C. / Chen, K.E. / Guo, Q. / Liu, M. / Evans, A.J. / Lewis, P.A. / Heesom, K.J. / Wilkinson, K.A. / Collins, B.M. / Cullen, P.J.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionAug 13, 2025ID: 8VOD
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Vacuolar protein sorting-associated protein 29
B: ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1973
Polymers23,0602
Non-polymers1371
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-6 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.899, 42.899, 172.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Isoform 2 of Vacuolar protein sorting-associated protein 29 / Vesicle protein sorting 29


Mass: 21089.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Isoform 2 of mouse Vps29 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Plasmid: pGEX4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QZ88
#2: Protein/peptide ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU / DENN domain-containing protein 4C


Mass: 1971.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5VZ89
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→37.15 Å / Num. obs: 11234 / % possible obs: 99.3 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.045 / Rrim(I) all: 0.101 / Χ2: 0.45 / Net I/σ(I): 7.1 / Num. measured all: 54772
Reflection shellResolution: 2.11→2.18 Å / % possible obs: 92.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.976 / Num. measured all: 3758 / Num. unique obs: 829 / CC1/2: 0.46 / Rpim(I) all: 0.503 / Rrim(I) all: 1.102 / Χ2: 0.24 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→36.32 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 840 10.14 %
Rwork0.1886 --
obs0.1951 8281 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 5 26 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.0562207
X-RAY DIFFRACTIONf_dihedral_angle_d5.812215
X-RAY DIFFRACTIONf_chiral_restr0.059254
X-RAY DIFFRACTIONf_plane_restr0.008281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.33781370.25871206X-RAY DIFFRACTION100
2.5-2.690.30811320.21011220X-RAY DIFFRACTION100
2.69-2.960.29941350.2631201X-RAY DIFFRACTION100
2.96-3.390.30641410.20881229X-RAY DIFFRACTION100
3.39-4.270.23941430.18111251X-RAY DIFFRACTION100
4.27-36.320.21061520.15481334X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -28.1934 Å / Origin y: 14.4034 Å / Origin z: -14.5937 Å
111213212223313233
T0.2129 Å20.0107 Å20.0237 Å2-0.3247 Å2-0.0187 Å2--0.3033 Å2
L1.2735 °2-0.1649 °20.768 °2-2.0902 °20.4203 °2--3.3328 °2
S-0.0182 Å °-0.1029 Å °0.0461 Å °0.0883 Å °-0.0978 Å °0.1221 Å °0.0744 Å °0.0391 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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