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- PDB-1o06: Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM) -

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Basic information

Entry
Database: PDB / ID: 1o06
TitleCrystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)
ComponentsVacuolar protein sorting-associated protein VPS27
KeywordsTRANSPORT PROTEIN / alpha-helix / coiled-coil / tetramer
Function / homology
Function and homology information


microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport ...microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / vacuolar membrane / protein secretion / ubiquitin binding / endosome membrane / endosome / protein heterodimerization activity / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 27
Similarity search - Component
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.45 Å
AuthorsFisher, R.D. / Wang, B. / Alam, S.L. / Higginson, D.S. / Rich, R. / Myszka, D. / Sundquist, W.I. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure and ubiquitin binding of the ubiquitin-interacting motif.
Authors: Fisher, R.D. / Wang, B. / Alam, S.L. / Higginson, D.S. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
History
DepositionFeb 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VPS27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4424
Polymers2,2451
Non-polymers1963
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Vacuolar protein sorting-associated protein VPS27
hetero molecules

A: Vacuolar protein sorting-associated protein VPS27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8838
Polymers4,4912
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area1300 Å2
ΔGint-75 kcal/mol
Surface area3310 Å2
MethodPISA
3
A: Vacuolar protein sorting-associated protein VPS27
hetero molecules

A: Vacuolar protein sorting-associated protein VPS27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8838
Polymers4,4912
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
Buried area530 Å2
ΔGint-66 kcal/mol
Surface area4080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.967, 34.967, 64.243
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-102-

ZN

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Components

#1: Protein/peptide Vacuolar protein sorting-associated protein VPS27


Mass: 2245.353 Da / Num. of mol.: 1 / Fragment: Residues 301-320 / Source method: obtained synthetically
Details: This sequence occurs naturally in Saccharomyces cerevisiae Vps27p and was synthesized by standard peptide synthesis methods
References: UniProt: P40343
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.98 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.6 mMVps27p-21drop
20.8 mMselenomethionine-substituted ubiquitin1drop
350 mMTris1droppH7.5
4150 mM1dropNaCl
50.08 Msodium cacodylate1reservoirpH6.5
60.16 Mzinc acetate1reservoir
710.4 %PEG80001reservoir
820 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2002
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 4525 / Num. obs: 4525 / % possible obs: 99.3 % / Observed criterion σ(I): -2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.5
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 10.5 / % possible all: 94.2
Reflection
*PLUS
Num. measured all: 32073
Reflection shell
*PLUS
% possible obs: 94.2 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→30.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.026 / SU ML: 0.041 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 443 9.9 %RANDOM
Rwork0.18535 ---
obs0.18884 4053 99.38 %-
all-4496 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.368 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms157 0 3 26 186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021174
X-RAY DIFFRACTIONr_bond_other_d0.0020.02146
X-RAY DIFFRACTIONr_angle_refined_deg1.3652.003236
X-RAY DIFFRACTIONr_angle_other_deg0.7333350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.116523
X-RAY DIFFRACTIONr_chiral_restr0.0510.225
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02211
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0226
X-RAY DIFFRACTIONr_nbd_refined0.3460.249
X-RAY DIFFRACTIONr_nbd_other0.2540.2177
X-RAY DIFFRACTIONr_nbtor_other0.0870.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2930.220
X-RAY DIFFRACTIONr_metal_ion_refined0.2050.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.211
X-RAY DIFFRACTIONr_mcbond_it0.6811.5113
X-RAY DIFFRACTIONr_mcangle_it1.342180
X-RAY DIFFRACTIONr_scbond_it2.418361
X-RAY DIFFRACTIONr_scangle_it4.264.556
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 30 -
Rwork0.248 262 -
obs--94.2 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.365

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