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- PDB-2rko: Crystal Structure of the Vps4p-dimer -

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Basic information

Entry
Database: PDB / ID: 2rko
TitleCrystal Structure of the Vps4p-dimer
ComponentsVacuolar protein sorting-associated protein 4Vacuole
KeywordsPROTEIN TRANSPORT / AAA-ATPase domain / ATP-binding / Endosome / Membrane / Nucleotide-binding / Phosphorylation / Transport
Function / homology
Function and homology information


ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / nucleus organization / endosomal transport / ATPase complex / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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 / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid 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 / 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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsHartmann, C. / Gruetter, M.G.
CitationJournal: J Mol Biol / Year: 2008
Title: Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p.
Authors: Claudia Hartmann / Mohamed Chami / Ulrich Zachariae / Bert L de Groot / Andreas Engel / Markus G Grütter /
Abstract: The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in ...The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in tumor suppression, apoptosis, and retrovirus budding. We present the first atomic structure of the nucleotide-free yeast His(6)DeltaNVps4p dimer and its AMPPNP (5'-adenylyl-beta,gamma-imidodiphosphate)-bound tetradecamer, derived from a cryo electron microscopy map. Vps4p dimers form two distinct heptameric rings and accommodate AAA cassettes in a head-to-head--not in a head-to-tail-fashion as in class II AAA-ATPases. Our model suggests a mechanism for disassembling ESCRT (endosomal sorting complex required for transport) complexes by movements of substrate-binding domains located at the periphery of the tetradecamer during ATP hydrolysis in one ring, followed by translocation through the central pore and ATP hydrolysis in the second ring.
History
DepositionOct 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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
A: Vacuolar protein sorting-associated protein 4


Theoretical massNumber of molelcules
Total (without water)36,6471
Polymers36,6471
Non-polymers00
Water0
1
A: Vacuolar protein sorting-associated protein 4

A: Vacuolar protein sorting-associated protein 4


Theoretical massNumber of molelcules
Total (without water)73,2952
Polymers73,2952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.116, 109.116, 176.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vacuolar protein sorting-associated protein 4 / Vacuole / VPS4P / Protein END13 / DOA4-independent degradation protein 6 / Vacuolar protein-targeting protein 10


Mass: 36647.418 Da / Num. of mol.: 1 / Fragment: AAA-ATPase domain, UNP residues 124-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS4P / Plasmid: pet20b(+) derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P52917
Sequence detailsTHIS IS A N-TERMINAL DELETION MUTANT (1-123) OF UNIPROT, P52917.

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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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.9
Details: 0.1M MES, 0.8M-1.9M MgSO4, pH 5.9-6.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→94.498 Å / Num. obs: 9446 / % possible obs: 99.4 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.35-3.538.40.444.91133813450.44100
3.53-3.758.40.2383.21069912730.238100
3.75-48.30.1455.11007512080.145100
4-4.328.30.0878.2934711240.087100
4.32-4.748.30.05412.5872610520.054100
4.74-5.38.20.04315.377729500.043100
5.3-6.1280.05910.368928630.059100
6.12-7.497.90.0836.957837310.083100
7.49-10.597.30.02915.643385930.02998.9
10.59-94.55.70.01926.917493070.01982.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3data extraction
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWI

1xwi


Resolution: 3.35→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.9 / SU B: 53.402 / SU ML: 0.388 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.993 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 471 5 %RANDOM
Rwork0.268 ---
obs0.27 9386 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 88.089 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å21.15 Å20 Å2
2--2.29 Å20 Å2
3----3.44 Å2
Refinement stepCycle: LAST / Resolution: 3.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 0 0 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221869
X-RAY DIFFRACTIONr_bond_other_d0.0020.021173
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9792539
X-RAY DIFFRACTIONr_angle_other_deg0.8332805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43825.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41915227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.295152
X-RAY DIFFRACTIONr_chiral_restr0.050.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.260.2611
X-RAY DIFFRACTIONr_nbd_other0.2080.21302
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21045
X-RAY DIFFRACTIONr_nbtor_other0.090.2949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.21
X-RAY DIFFRACTIONr_mcbond_it2.7671.51675
X-RAY DIFFRACTIONr_mcbond_other0.5021.5560
X-RAY DIFFRACTIONr_mcangle_it3.81322067
X-RAY DIFFRACTIONr_scbond_it5.693612
X-RAY DIFFRACTIONr_scangle_it7.9764.5472
LS refinement shellResolution: 3.35→3.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 34 -
Rwork0.324 630 -
all-664 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 29.5343 Å / Origin y: 20.0701 Å / Origin z: 9.427 Å
111213212223313233
T-0.2001 Å2-0.131 Å2-0.1284 Å2--0.3411 Å2-0.0423 Å2---0.4068 Å2
L1.4178 °2-0.3439 °2-0.2649 °2-9.3412 °2-0.0197 °2--0.5794 °2
S-0.1375 Å °-0.3605 Å °0.3196 Å °0.6917 Å °-0.1432 Å °0.2121 Å °0.1474 Å °-0.1838 Å °0.2807 Å °
Xplor fileSerial no: 1 / Param file: protein_rep.param

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