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- PDB-4u7e: The crystal structure of the complex of LIP5 NTD and IST1 MIM -

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Basic information

Entry
Database: PDB / ID: 4u7e
TitleThe crystal structure of the complex of LIP5 NTD and IST1 MIM
Components
  • IST1 homolog
  • Vacuolar protein sorting-associated protein VTA1 homolog
KeywordsPROTEIN TRANSPORT / Complex / MIM1
Function / homology
Function and homology information


MIT domain binding / ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / collateral sprouting / positive regulation of collateral sprouting / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body assembly ...MIT domain binding / ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / collateral sprouting / positive regulation of collateral sprouting / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body assembly / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / azurophil granule lumen / intracellular protein localization / nuclear envelope / protein transport / midbody / endosome membrane / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein vta1 / 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 Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway ...Vacuolar protein sorting-associated protein vta1 / 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 Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
IST1 homolog / Vacuolar protein sorting-associated protein VTA1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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 / 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

Downloads & links

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Assembly

Deposited unit
B: Vacuolar protein sorting-associated protein VTA1 homolog
A: IST1 homolog


Theoretical massNumber of molelcules
Total (without water)21,8022
Polymers21,8022
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.315, 65.578, 78.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein VTA1 homolog / Dopamine-responsive gene 1 protein / DRG-1 / LYST-interacting protein 5 / LIP5 / SKD1-binding protein 1 / SBP1


Mass: 18792.727 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-162)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTA1, C6orf55, HSPC228, My012 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NP79
#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.: 210 / 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: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% (w/v) PEG5000MME, 0.1 M ammonium sulfate , 0.1 M MES
PH range: 7

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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: 1.6→33.69 Å / Num. obs: 22717 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.5
Reflection shellRedundancy: 7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: dev_1593)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.69 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 1143 5.03 %
Rwork0.1775 --
obs0.1787 22717 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 0 210 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091401
X-RAY DIFFRACTIONf_angle_d1.2831894
X-RAY DIFFRACTIONf_dihedral_angle_d10.478502
X-RAY DIFFRACTIONf_chiral_restr0.053212
X-RAY DIFFRACTIONf_plane_restr0.007243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.67240.2281320.1812608X-RAY DIFFRACTION99
1.6724-1.76050.21451490.18332641X-RAY DIFFRACTION100
1.7605-1.87080.23811330.18352664X-RAY DIFFRACTION100
1.8708-2.01530.21941320.17622702X-RAY DIFFRACTION100
2.0153-2.2180.20531450.16892655X-RAY DIFFRACTION100
2.218-2.53890.19881470.1782706X-RAY DIFFRACTION100
2.5389-3.19830.1931520.18312731X-RAY DIFFRACTION100
3.1983-33.690.18831530.17472867X-RAY DIFFRACTION100

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