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- PDB-5gtu: Structural and mechanistic insights into regulation of the retrom... -

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Basic information

Entry
Database: PDB / ID: 5gtu
TitleStructural and mechanistic insights into regulation of the retromer coat by TBC1d5
Components
  • TBC1 domain family member 5
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsHYDROLASE / complex / cellular trafficking / endosomal sorting
Function / homology
Function and homology information


retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / AP-2 adaptor complex binding / retromer complex binding / retromer complex / endocytic recycling / activation of GTPase activity / retrograde transport, endosome to Golgi / response to starvation / positive regulation of receptor internalization ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / AP-2 adaptor complex binding / retromer complex binding / retromer complex / endocytic recycling / activation of GTPase activity / retrograde transport, endosome to Golgi / response to starvation / positive regulation of receptor internalization / autophagosome / GTPase activator activity / macroautophagy / intracellular protein transport / autophagy / late endosome / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / protein-containing complex binding / Golgi apparatus / metal ion binding / cytosol
Similarity search - Function
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases ...Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TBC1 domain family member 5 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJia, D. / Rosen, M.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056322 United States
Howard Hughes Medical Institute United States
CNSFJunior One Thousand Talents program China
Welch FoundationI-1544 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structural and mechanistic insights into regulation of the retromer coat by TBC1d5
Authors: Jia, D. / Zhang, J.S. / Li, F. / Wang, J. / Deng, Z. / White, M.A. / Osborne, D.G. / Phillips-Krawczak, C. / Gomez, T.S. / Li, H. / Singla, A. / Burstein, E. / Billadeau, D.D. / Rosen, M.K.
History
DepositionAug 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 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: TBC1 domain family member 5


Theoretical massNumber of molelcules
Total (without water)24,1402
Polymers24,1402
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-15 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.881, 63.832, 78.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole / hVPS29 / PEP11 homolog / Vesicle protein sorting 29


Mass: 20955.174 Da / Num. of mol.: 1 / Fragment: UNP residues 2-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#2: Protein/peptide TBC1 domain family member 5


Mass: 3184.448 Da / Num. of mol.: 1 / Fragment: UNP residues 132-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D5, KIAA0210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92609
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6
Details: 0.1M Bis-Tris, pH6.0, 2% Tacsimate, pH 6.0, 15~20% PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 33729 / % possible obs: 98.12 % / Redundancy: 5.7 % / Net I/σ(I): 38

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z2X

1z2x


Resolution: 1.5→39.01 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.122 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18555 1407 4 %RANDOM
Rwork0.13905 ---
obs0.14089 33729 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0 Å2
2---0.81 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 0 140 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191710
X-RAY DIFFRACTIONr_bond_other_d0.0040.021654
X-RAY DIFFRACTIONr_angle_refined_deg2.2881.952314
X-RAY DIFFRACTIONr_angle_other_deg1.20133807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.30525.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50715298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.075155
X-RAY DIFFRACTIONr_chiral_restr0.1690.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02393
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5231.828838
X-RAY DIFFRACTIONr_mcbond_other2.5021.826837
X-RAY DIFFRACTIONr_mcangle_it3.0042.7381044
X-RAY DIFFRACTIONr_mcangle_other3.0042.7411045
X-RAY DIFFRACTIONr_scbond_it3.9572.255872
X-RAY DIFFRACTIONr_scbond_other3.9592.258873
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3063.231271
X-RAY DIFFRACTIONr_long_range_B_refined4.39216.1611971
X-RAY DIFFRACTIONr_long_range_B_other4.21815.7541919
X-RAY DIFFRACTIONr_rigid_bond_restr4.83233364
X-RAY DIFFRACTIONr_sphericity_free26.526546
X-RAY DIFFRACTIONr_sphericity_bonded8.52953420
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 89 -
Rwork0.296 2016 -
obs--81.62 %
Refinement TLS params.Method: refined / Origin x: 16.0945 Å / Origin y: -3.7984 Å / Origin z: -8.6209 Å
111213212223313233
T0.0168 Å20.0079 Å20.0122 Å2-0.005 Å20.0142 Å2--0.0744 Å2
L1.5928 °20.1403 °20.251 °2-1.5645 °2-0.3021 °2--1.6338 °2
S-0.0251 Å °0.0213 Å °0.1383 Å °0.065 Å °0.0222 Å °0.0535 Å °-0.1492 Å °-0.0606 Å °0.0029 Å °

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