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- PDB-2fau: Crystal structure of human vps26 -

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Basic information

Entry
Database: PDB / ID: 2fau
TitleCrystal structure of human vps26
ComponentsVacuolar protein sorting 26
KeywordsPROTEIN TRANSPORT / ARRESTIN / RETROMER
Function / homology
Function and homology information


tubular endosome / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / regulation of macroautophagy / intracellular protein transport / vesicle / early endosome ...tubular endosome / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / regulation of macroautophagy / intracellular protein transport / vesicle / early endosome / lysosome / endosome membrane / endosome / cytosol
Similarity search - Function
Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Immunoglobulin-like - #640 / Arrestin-like, C-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 Å
AuthorsShi, H. / Rojas, R. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: The retromer subunit Vps26 has an arrestin fold and binds Vps35 through its C-terminal domain.
Authors: Shi, H. / Rojas, R. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1032
Polymers40,0111
Non-polymers921
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.964, 76.368, 126.491
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 26 / Vesicle protein sorting 26 / hVPS26


Mass: 40010.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Plasmid: pmr101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: O75436
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG 8000 100mM Na cacodylate pH 6.5 15% glycerol 10mM DTT 1mM TmCl3, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1981
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.072 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 6, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
3Si 111 CHANNELMADMx-ray1
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.09→48.71 Å / Num. all: 22533 / Num. obs: 22533 / % possible obs: 87.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21 Å2
Reflection shellResolution: 2.09→2.16 Å / % possible all: 55.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.1→48.71 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 860282.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2119 10 %RANDOM
Rwork0.235 ---
all0.2282 21275 --
obs0.235 21275 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0291 Å2 / ksol: 0.342588 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1-17.16 Å20 Å20 Å2
2---1.34 Å20 Å2
3----15.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 6 82 2471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 247 10.5 %
Rwork0.348 2105 -
obs--59.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4caf.parcaf.top
X-RAY DIFFRACTION5gol_xplor_par.txtgol_xplor_top.txt

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