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- PDB-1elk: VHS domain of TOM1 protein from H. sapiens -

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Basic information

Entry
Database: PDB / ID: 1elk
TitleVHS domain of TOM1 protein from H. sapiens
ComponentsTARGET OF MYB1
KeywordsENDOCYTOSIS/EXOCYTOSIS / Superhelix of helices / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / endosomal transport / azurophil granule membrane / clathrin binding ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / endosomal transport / azurophil granule membrane / clathrin binding / polyubiquitin modification-dependent protein binding / specific granule membrane / ubiquitin binding / endocytosis / protein transport / early endosome membrane / early endosome / endosome / endosome membrane / Neutrophil degranulation / Golgi apparatus / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 ...Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Target of Myb1 membrane trafficking protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsMisra, S. / Beach, B. / Hurley, J.H.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes
Authors: Misra, S. / Beach, B. / Hurley, J.H.
#1: Journal: FEBS Lett. / Year: 1998
Title: VHS domain marks a group of proteins involved in endocytosis and vesicular trafficking.
Authors: Lohi, O. / Lehto, V.P.
History
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TARGET OF MYB1
B: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)34,9682
Polymers34,9682
Non-polymers00
Water6,792377
1
A: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.07, 52.86, 73.22
Angle α, β, γ (deg.)90.0, 99.75, 90.0
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly unknown; dimer within asymmetric unit is likely nonbiological

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Components

#1: Protein TARGET OF MYB1


Mass: 17484.029 Da / Num. of mol.: 2 / Fragment: VHS DOMAIN / Mutation: M1G; C-TERMINAL CLONING ARTIFACT GAM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid details: PARALLEL PHIS2 (SHEFFIELD P, GARRARD S, DEREWENDA Z.,PROTEIN EXPR PURIF. 1999, 15(1):34-99
Plasmid: PHIS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O60784
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%PEG8000, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropNaCl
220 mMTris-HCl1drop
30.1 mMEDTA1drop
410 mMdithiothreitol1drop
512-18 mg/mlprotain1drop
620 %PEG80001reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793
DetectorType: ADSC / Detector: CCD / Date: Nov 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 49338 / Num. obs: 49338 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.36 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.276 / % possible all: 94.8
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 94.8 % / Num. unique obs: 4775 / Mean I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9refinement
CNS0.9phasing
RefinementResolution: 1.5→15.67 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 4722 Random
Rwork0.193 --
all0.201 48257 -
obs0.201 48257 -
Refinement stepCycle: LAST / Resolution: 1.5→15.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 0 377 2787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_torsion_impr_deg1.38
X-RAY DIFFRACTIONc_torsion_deg21.2
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 10 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor Rfree: 0.214 / Rfactor obs: 0.174

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