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- PDB-4txq: Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM -

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Basic information

Entry
Database: PDB / ID: 4txq
TitleCrystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM
Components
  • Charged multivesicular body protein 1b
  • Vacuolar protein sorting-associated protein VTA1 homologVacuole
KeywordsPROTEIN TRANSPORT / MIT / MIT domain / ESCRT
Function / homology
Function and homology information


MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway ...MIT domain binding / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / membrane coat / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / nucleus organization / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / midbody / endosome membrane / cell division / lysosomal membrane / protein domain specific binding / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / 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 / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Charged multivesicular body protein 1b / Vacuolar protein sorting-associated protein VTA1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsVild, C.J. / Xu, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F027259 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5.
Authors: Vild, C.J. / Li, Y. / Guo, E.Z. / Liu, Y. / Xu, Z.
History
DepositionJul 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
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 1.4Sep 27, 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 / 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: Vacuolar protein sorting-associated protein VTA1 homolog
B: Vacuolar protein sorting-associated protein VTA1 homolog
C: Charged multivesicular body protein 1b
D: Charged multivesicular body protein 1b


Theoretical massNumber of molelcules
Total (without water)43,0234
Polymers43,0234
Non-polymers00
Water3,567198
1
A: Vacuolar protein sorting-associated protein VTA1 homolog
C: Charged multivesicular body protein 1b


Theoretical massNumber of molelcules
Total (without water)21,5122
Polymers21,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-1 kcal/mol
Surface area9650 Å2
MethodPISA
2
B: Vacuolar protein sorting-associated protein VTA1 homolog
D: Charged multivesicular body protein 1b


Theoretical massNumber of molelcules
Total (without water)21,5122
Polymers21,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.936, 55.536, 195.359
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 / Vacuole / Dopamine-responsive gene 1 protein / DRG-1 / LYST-interacting protein 5 / LIP5 / SKD1-binding protein 1 / SBP1


Mass: 18792.727 Da / Num. of mol.: 2 / Fragment: UNP residues 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTA1, C6orf55, HSPC228, My012 / Plasmid: pSMT3
Details (production host): modified pET28b; his6-sumo tag; kanR
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NP79
#2: Protein/peptide Charged multivesicular body protein 1b / CHMP1.5 / Chromatin-modifying protein 1b / CHMP1b / Vacuolar protein sorting-associated protein 46- ...CHMP1.5 / Chromatin-modifying protein 1b / CHMP1b / Vacuolar protein sorting-associated protein 46-2 / hVps46-2


Mass: 2718.953 Da / Num. of mol.: 2 / Fragment: UNP residues 176-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1B, C18orf2 / Plasmid: pSMT3
Details (production host): modified pET28b; his6-sumo tag; kanR
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q7LBR1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2012
RadiationMonochromator: diamond laue monochromators with beryllium lenses
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.208→41.076 Å / Num. obs: 29702 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.4
Reflection shellResolution: 2.208→2.28 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TXP

4txp


Resolution: 2.21→41.076 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1996 6.74 %Random selection
Rwork0.1932 ---
obs0.1955 29633 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→41.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 198 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092866
X-RAY DIFFRACTIONf_angle_d1.2243870
X-RAY DIFFRACTIONf_dihedral_angle_d10.4261072
X-RAY DIFFRACTIONf_chiral_restr0.051429
X-RAY DIFFRACTIONf_plane_restr0.006499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.26340.28141270.24761766X-RAY DIFFRACTION92
2.2634-2.32460.27861400.22711972X-RAY DIFFRACTION100
2.3246-2.3930.25521400.22191960X-RAY DIFFRACTION100
2.393-2.47020.31111320.20841936X-RAY DIFFRACTION100
2.4702-2.55850.24031510.21421965X-RAY DIFFRACTION100
2.5585-2.66090.26121390.2061974X-RAY DIFFRACTION100
2.6609-2.7820.24061400.20211974X-RAY DIFFRACTION100
2.782-2.92860.23121460.18991966X-RAY DIFFRACTION100
2.9286-3.1120.21521420.19521956X-RAY DIFFRACTION100
3.112-3.35220.2161390.20741988X-RAY DIFFRACTION100
3.3522-3.68940.25461450.19031996X-RAY DIFFRACTION100
3.6894-4.22270.21421460.17352011X-RAY DIFFRACTION100
4.2227-5.31840.17951510.17372039X-RAY DIFFRACTION100
5.3184-41.08330.22361580.19172134X-RAY DIFFRACTION99

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