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- PDB-2v6x: Stractural insight into the interaction between ESCRT-III and Vps4 -

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Basic information

Entry
Database: PDB / ID: 2v6x
TitleStractural insight into the interaction between ESCRT-III and Vps4
Components
  • DOA4-INDEPENDENT DEGRADATION PROTEIN 4
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4Vacuole
KeywordsPROTEIN TRANSPORT / VACUOLE / ENDOSOME / TRANSPORT / ESCRT-III / MVB / VPS2 / VPS4 / SKD1 / VPS4B / VPS4A / CHMP2B / CHMP2A / NUCLEOTIDE-BINDING / AAA-ATPASE / ATP-BINDING / MULTIVESICULAR / VACUOLAR PROTEIN SORTING
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 / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway ...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 / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vacuole organization / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / reticulophagy / endosomal transport / ATPase complex / nucleus organization / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Snf7 family / Snf7 / Vps4 C terminal oligomerisation domain ...Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Snf7 family / Snf7 / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Mainly Alpha
Similarity search - Domain/homology
DOA4-independent degradation protein 4 / Vacuolar protein sorting-associated protein 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsObita, T. / Perisic, O. / Ghazi-Tabatabai, S. / Saksena, S. / Emr, S.D. / Williams, R.L.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for Selective Recognition of Escrt-III by the Aaa ATPase Vps4
Authors: Obita, T. / Saksena, S. / Ghazi-Tabatabai, S. / Gill, D.J. / Perisic, O. / Emr, S.D. / Williams, R.L.
History
DepositionJul 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
B: DOA4-INDEPENDENT DEGRADATION PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6853
Polymers15,5892
Non-polymers961
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-18.2 kcal/mol
Surface area9990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.145, 82.270, 21.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4 / Vacuole / VPS4 / PROTEIN END13 / DOA4-INDEPENDENT DEGRADATION PROTEIN 6 / VACUOLAR PROTEIN-TARGETING PROTEIN 10


Mass: 9816.693 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN RESIUDES 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPTG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P52917, vesicle-fusing ATPase
#2: Protein DOA4-INDEPENDENT DEGRADATION PROTEIN 4 / VACUOLAR PROTEIN SORTING- ASSOCIATED PROTEIN 2 / VPS2 / VACUOLAR PROTEIN-TARGETING PROTEIN 14


Mass: 5772.053 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT RESIDUES 102-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPTG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P36108
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 36.1 % / Description: NONE
Crystal growpH: 7 / Details: 0.1M HEPES(PH7.0), 2.0M AMMONIUM SULFATE

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.8726, 0.9392
SYNCHROTRONESRF ID23-220.9792, 0.9796
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 26, 2007
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.93921
30.97921
40.97961
ReflectionResolution: 2→56.61 Å / Num. obs: 9997 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.23 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.02 Å / Redundancy: 5.31 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.28 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata reduction
TRUNCATEdata scaling
SHARPphasing
ARP/wARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.98→56.61 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.393 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SEGMENT 207-216 OF VPS2 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 477 4.8 %RANDOM
Rwork0.198 ---
obs0.2 9483 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--1.52 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.98→56.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 0 5 32 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9861343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79926.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.964153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02731
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2391
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.2681
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9341.5639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3722980
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7313410
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.854.5363
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 18
Rwork0.216 385
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.53110.6238-0.33111.56480.35050.6999-0.075-0.05020.0999-0.10980.125-0.00490.0223-0.0197-0.0499-0.03890.00250.0001-0.0390.0291-0.090132.284225.440438.2005
225.8261-6.6176-10.52813.34463.33695.35480.742-0.58270.918-0.2828-0.293-0.2684-0.48130.078-0.449-0.0857-0.012-0.0028-0.049-0.0515-0.083152.244829.599243.9663
325.96069.5524.03578.2359-1.18267.544-0.5471-0.2061-1.4406-0.5140.3731-0.67390.0957-0.05460.174-0.0869-0.00440.0179-0.0170.0031-0.128832.094316.235446.8005
430.04628.38242.303927.3093-0.86593.9751-1.79871.71282.7235-1.46461.87752.4026-0.6202-0.0698-0.07890.0489-0.1903-0.2899-0.06390.31150.220827.94535.496835.356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 80
2X-RAY DIFFRACTION2B181 - 194
3X-RAY DIFFRACTION3B195 - 206
4X-RAY DIFFRACTION4B217 - 231

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