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- PDB-4txp: Crystal structure of LIP5 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4txp
TitleCrystal structure of LIP5 N-terminal domain
ComponentsVacuolar protein sorting-associated protein VTA1 homolog
KeywordsPROTEIN TRANSPORT / MIT / MIT domain / ESCRT
Function / homology
Function and homology information


ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / multivesicular body sorting pathway / multivesicular body assembly / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / macroautophagy / Budding and maturation of HIV virion / protein transport / endosome membrane ...ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / multivesicular body sorting pathway / multivesicular body assembly / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / macroautophagy / Budding and maturation of HIV virion / protein transport / endosome membrane / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein VTA1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.01 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 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid
Remark 0 : statistics at the very beginning when nothing is done yet

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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: Vacuolar protein sorting-associated protein VTA1 homolog


Theoretical massNumber of molelcules
Total (without water)56,3783
Polymers56,3783
Non-polymers00
Water61334
1
A: Vacuolar protein sorting-associated protein VTA1 homolog


Theoretical massNumber of molelcules
Total (without water)18,7931
Polymers18,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar protein sorting-associated protein VTA1 homolog


Theoretical massNumber of molelcules
Total (without water)18,7931
Polymers18,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Vacuolar protein sorting-associated protein VTA1 homolog


Theoretical massNumber of molelcules
Total (without water)18,7931
Polymers18,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.381, 76.381, 355.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: diamond laue monochromators with beryllium lenses
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.01→48.46 Å / Num. obs: 13124 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 86.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 3.01→3.25 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 3.01→48.46 Å / Cor.coef. Fo:Fc: 0.9041 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.449
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 643 4.95 %RANDOM
Rwork0.2484 ---
obs0.2502 12993 98.85 %-
Displacement parametersBiso mean: 71.11 Å2
Baniso -1Baniso -2Baniso -3
1-5.9946 Å20 Å20 Å2
2--5.9946 Å20 Å2
3----11.9891 Å2
Refine analyzeLuzzati coordinate error obs: 0.666 Å
Refinement stepCycle: 1 / Resolution: 3.01→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 34 3368
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013406HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064631HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1061SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes525HARMONIC5
X-RAY DIFFRACTIONt_it3406HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion19.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3979SEMIHARMONIC4
LS refinement shellResolution: 3.01→3.25 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3689 146 5.62 %
Rwork0.2776 2452 -
all0.2826 2598 -
obs--98.85 %

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