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- PDB-4u7y: Structure of the complex of VPS4B MIT and IST1 MIM -

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Basic information

Entry
Database: PDB / ID: 4u7y
TitleStructure of the complex of VPS4B MIT and IST1 MIM
Components
  • IST1 homolog
  • Vacuolar protein sorting-associated protein 4B
KeywordsPROTEIN TRANSPORT / complex / MIM1
Function / homology
Function and homology information


protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting ...protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / MIT domain binding / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / regulation of centrosome duplication / nuclear membrane reassembly / establishment of blood-brain barrier / positive regulation of collateral sprouting / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / vacuole organization / positive regulation of exosomal secretion / midbody abscission / membrane fission / plasma membrane repair / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endosome to lysosome transport via multivesicular body sorting pathway / cholesterol transport / regulation of mitotic spindle assembly / Flemming body / vesicle-fusing ATPase / endosomal transport / mitotic metaphase chromosome alignment / response to lipid / ATPase complex / nucleus organization / viral budding via host ESCRT complex / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / autophagosome maturation / canonical Wnt signaling pathway / nuclear pore / positive regulation of G2/M transition of mitotic cell cycle / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / macroautophagy / establishment of protein localization / potassium ion transport / Budding and maturation of HIV virion / autophagy / spindle pole / azurophil granule lumen / late endosome membrane / intracellular protein localization / nuclear envelope / protein transport / midbody / angiogenesis / endosome / endosome membrane / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / protein homodimerization activity / ATP hydrolysis activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain ...Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / 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 / 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
Vacuolar protein sorting-associated protein 4B / IST1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsGuo, E.Z. / Xu, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095769 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains.
Authors: Guo, E.Z. / Xu, Z.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4B
B: IST1 homolog


Theoretical massNumber of molelcules
Total (without water)13,3202
Polymers13,3202
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area6070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.401, 78.401, 67.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Vacuolar protein sorting-associated protein 4B / Cell migration-inducing gene 1 protein / Suppressor of K(+) transport growth defect 1 / Protein SKD1


Mass: 10310.705 Da / Num. of mol.: 1 / Fragment: MIT domain (UNP residues 1-89)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4B, SKD1, VPS42, MIG1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O75351, vesicle-fusing ATPase
#2: Protein/peptide IST1 homolog / hIST1 / Putative MAPK-activating protein PM28


Mass: 3009.262 Da / Num. of mol.: 1 / Fragment: UNP residues 341-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P53990
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 2.58 M Na-malonate / PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→33.82 Å / Num. obs: 4455 / % possible obs: 96.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 21.1
Reflection shellRedundancy: 12.7 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 6.4 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: dev_1593)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WR0

1wr0


Resolution: 2.502→33.82 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 226 5.07 %
Rwork0.2252 --
obs0.2276 4455 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms716 0 0 6 722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007725
X-RAY DIFFRACTIONf_angle_d0.997978
X-RAY DIFFRACTIONf_dihedral_angle_d16.239253
X-RAY DIFFRACTIONf_chiral_restr0.038111
X-RAY DIFFRACTIONf_plane_restr0.004126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-3.1520.37121030.24852071X-RAY DIFFRACTION98
3.152-33.82410.23551230.21582158X-RAY DIFFRACTION96

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