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- PDB-4u7i: Structure of the complex of Spartin MIT and IST1 MIM -

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Basic information

Entry
Database: PDB / ID: 4u7i
TitleStructure of the complex of Spartin MIT and IST1 MIM
Components
  • IST1 homolog
  • Spartin
KeywordsPROTEIN TRANSPORT / Complex / MIM3
Function / homology
Function and homology information


negative regulation of collateral sprouting in absence of injury / viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / lipid droplet organization ...negative regulation of collateral sprouting in absence of injury / viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / lipid droplet organization / multivesicular body assembly / collateral sprouting in absence of injury / Flemming body / neuromuscular process / positive regulation of proteolysis / negative regulation of BMP signaling pathway / viral release from host cell / endoplasmic reticulum-Golgi intermediate compartment / adipose tissue development / BMP signaling pathway / lipid droplet / regulation of mitochondrial membrane potential / establishment of protein localization / protein localization / azurophil granule lumen / protein transport / nuclear envelope / midbody / mitochondrial outer membrane / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / chromatin / Neutrophil degranulation / protein-containing complex binding / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Senescence/spartin-associated, C-terminal / Spartin-like / Senescence domain / Vacuolar protein sorting-associated protein Ist1 / Regulator of Vps4 activity in the MVB pathway / Vacuolar protein sorting-associated protein IST1-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain ...Senescence/spartin-associated, C-terminal / Spartin-like / Senescence domain / Vacuolar protein sorting-associated protein Ist1 / Regulator of Vps4 activity in the MVB pathway / Vacuolar protein sorting-associated protein IST1-like / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / MIT domain / Microtubule Interacting and Trafficking molecule domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IST1 homolog / Spartin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 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 30, 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
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_oper_list.symmetry_operation
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spartin
B: IST1 homolog


Theoretical massNumber of molelcules
Total (without water)13,8042
Polymers13,8042
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.257, 46.257, 115.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

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Components

#1: Protein Spartin / Spastic paraplegia 20 protein / Trans-activated by hepatitis C virus core protein 1


Mass: 10794.293 Da / Num. of mol.: 1 / Fragment: MIT domain (UNP residues 8-101)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPG20, KIAA0610, TAHCCP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8N0X7
#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 / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 2.9 M Na-malonate / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97828 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97828 Å / Relative weight: 1
ReflectionResolution: 1.79→29.61 Å / Num. obs: 12400 / % possible obs: 99.6 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 43
Reflection shellRedundancy: 8.4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 4 / % possible all: 100

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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: 2DL1
Resolution: 1.794→29.61 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 598 4.82 %
Rwork0.1902 --
obs0.1916 12400 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.794→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 100 964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006875
X-RAY DIFFRACTIONf_angle_d0.9421170
X-RAY DIFFRACTIONf_dihedral_angle_d13.703337
X-RAY DIFFRACTIONf_chiral_restr0.037127
X-RAY DIFFRACTIONf_plane_restr0.005152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.794-1.97420.27281580.1952867X-RAY DIFFRACTION100
1.9742-2.25980.22351470.19192893X-RAY DIFFRACTION100
2.2598-2.84670.22861570.21242936X-RAY DIFFRACTION100
2.8467-29.61360.20951360.18063106X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.3844 Å / Origin y: 6.1248 Å / Origin z: -7.1335 Å
111213212223313233
T0.1889 Å2-0.0083 Å2-0.009 Å2-0.1303 Å20.0173 Å2--0.2132 Å2
L1.8436 °20.1574 °2-0.1277 °2-1.878 °2-1.6184 °2--5.5086 °2
S0.0032 Å °-0.1122 Å °-0.074 Å °0.0177 Å °-0.0414 Å °0.0048 Å °-0.1073 Å °0.1448 Å °0.0114 Å °
Refinement TLS groupSelection details: all

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