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- PDB-3mhv: Crystal Structure of Vps4 and Vta1 -

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Basic information

Entry
Database: PDB / ID: 3mhv
TitleCrystal Structure of Vps4 and Vta1
Components
  • Vacuolar protein sorting-associated protein 4
  • Vacuolar protein sorting-associated protein VTA1
KeywordsPROTEIN TRANSPORT / vps4 / vta1 / AAA / ATPase / ESCRT / MVB / sorting
Function / homology
Function and homology information


ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / multivesicular body sorting pathway ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / lipid transport / ATPase complex / nucleus organization / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / protein-macromolecule adaptor activity / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal ...Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Immunoglobulin FC, subunit C / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYang, D. / Hurley, J.H.
CitationJournal: Structure / Year: 2010
Title: Structural role of the Vps4-Vta1 interface in ESCRT-III recycling
Authors: Yang, D. / Hurley, J.H.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Vacuolar protein sorting-associated protein 4
A: Vacuolar protein sorting-associated protein VTA1


Theoretical massNumber of molelcules
Total (without water)17,5262
Polymers17,5262
Non-polymers00
Water00
1
C: Vacuolar protein sorting-associated protein 4
A: Vacuolar protein sorting-associated protein VTA1

C: Vacuolar protein sorting-associated protein 4
A: Vacuolar protein sorting-associated protein VTA1


Theoretical massNumber of molelcules
Total (without water)35,0514
Polymers35,0514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)37.979, 70.322, 88.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Vacuolar protein sorting-associated protein 4 / Vps4 / Protein END13 / DOA4-independent degradation protein 6 / Vacuolar protein-targeting protein 10


Mass: 12814.344 Da / Num. of mol.: 1 / Fragment: residues 297-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS4 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P52917
#2: Protein/peptide Vacuolar protein sorting-associated protein VTA1 / VPS20-associated protein 1


Mass: 4711.369 Da / Num. of mol.: 1 / Fragment: residues 289-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTA1 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: Q06263

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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: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion
Details: 16%-24% PEG3350, 0.1-0.3M sodium formate, VAPOR DIFFUSION, temperature 288K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9719 Å
DetectorDetector: CCD / Date: Mar 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9719 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 3803 / % possible obs: 80 % / Redundancy: 3.7 % / Rsym value: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 144 / Rsym value: 0.355 / % possible all: 62.1

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 3EIE and 2RKL

3eie

2rkl


Resolution: 3.1→37.98 Å / Rfactor Rfree error: 0.025 / Data cutoff high absF: 1127778.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THe structure was refined also with refmac 5.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 189 5 %RANDOM
Rwork0.298 ---
obs0.311 3761 80.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0117 Å2 / ksol: 0.272677 e/Å3
Displacement parametersBiso mean: 106.3 Å2
Baniso -1Baniso -2Baniso -3
1--29.41 Å20 Å20 Å2
2--0.64 Å20 Å2
3---28.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.76 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 3.1→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 0 0 1099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.6
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: 3.1→3.29 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 22 4.5 %
Rwork0.435 464 -
obs--66.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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