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- PDB-4txr: Crystal structure of LIP5 N-terminal domain complexed with CHMP1B... -

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Basic information

Entry
Database: PDB / ID: 4txr
TitleCrystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM
Components
  • (Charged multivesicular body protein ...) x 2
  • Vacuolar protein sorting-associated protein VTA1 homolog
KeywordsPROTEIN TRANSPORT / MIT domain / MIM / ESCRT
Function / homology
Function and homology information


MIT domain binding / viral budding / multivesicular body-lysosome fusion / amphisome membrane / 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 ...MIT domain binding / viral budding / multivesicular body-lysosome fusion / amphisome membrane / 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 / cellular response to muramyl dipeptide / regulation of centrosome duplication / nuclear membrane reassembly / multivesicular body sorting pathway / membrane coat / vesicle budding from membrane / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / regulation of mitotic spindle assembly / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / regulation of receptor recycling / autophagosome maturation / nuclear pore / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / erythrocyte differentiation / macroautophagy / establishment of protein localization / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / cellular response to lipopolysaccharide / midbody / endosome membrane / cadherin binding / protein domain specific binding / lysosomal membrane / cell division / 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
ACETATE ION / Charged multivesicular body protein 1b / Vacuolar protein sorting-associated protein VTA1 homolog / Charged multivesicular body protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Mar 25, 2015Group: Database references
Revision 2.0Dec 4, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity_src_gen / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.auth_seq_num / _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_site_gen.auth_seq_id
Revision 2.1Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Charged multivesicular body protein 1b
A: Vacuolar protein sorting-associated protein VTA1 homolog
C: Charged multivesicular body protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31813
Polymers27,7003
Non-polymers61810
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-13 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.197, 60.567, 52.048
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Charged multivesicular body protein ... , 2 types, 2 molecules BC

#1: 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.: 1 / 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: Protein Charged multivesicular body protein 5 / Chromatin-modifying protein 5 / SNF7 domain-containing protein 2 / Vacuolar protein sorting- ...Chromatin-modifying protein 5 / SNF7 domain-containing protein 2 / Vacuolar protein sorting-associated protein 60 / hVps60


Mass: 6188.371 Da / Num. of mol.: 1 / Fragment: UNP residues 139-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CHMP5, C9orf83, SNF7DC2, CGI-34, HSPC177, PNAS-114, PNAS-2
Plasmid: pSMT3
Details (production host): modified pET28B; his6-SUMO tag; kanR
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NZZ3

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Protein , 1 types, 1 molecules A

#2: 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: 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

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Non-polymers , 3 types, 289 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Description: approximately 150 nanometer large diamond shaped crystal
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 19% PEG 4000, 0.025 M sodium acetate

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99983 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: diamond laue monochromators with beryllium lenses
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 1→28.68 Å / Num. obs: 99846 / % possible obs: 87.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 50.6
Reflection shellResolution: 1→1.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / % possible all: 46.1

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Processing

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

4txq


Resolution: 1→28.668 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 1981 1.98 %Random selection
Rwork0.1639 ---
obs0.1642 99807 87.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→28.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 40 279 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082128
X-RAY DIFFRACTIONf_angle_d1.1472898
X-RAY DIFFRACTIONf_dihedral_angle_d13.267858
X-RAY DIFFRACTIONf_chiral_restr0.065307
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0002-1.02520.2593710.24843413X-RAY DIFFRACTION43
1.0252-1.05290.2273960.20434922X-RAY DIFFRACTION62
1.0529-1.08390.21281380.19016962X-RAY DIFFRACTION87
1.0839-1.11890.16091360.18487159X-RAY DIFFRACTION90
1.1189-1.15880.19121540.17787222X-RAY DIFFRACTION90
1.1588-1.20520.18771500.17837250X-RAY DIFFRACTION91
1.2052-1.26010.19121490.17667319X-RAY DIFFRACTION92
1.2601-1.32650.20581470.17157409X-RAY DIFFRACTION93
1.3265-1.40960.18211580.1697462X-RAY DIFFRACTION94
1.4096-1.51850.18841570.16877542X-RAY DIFFRACTION94
1.5185-1.67130.1931520.16417631X-RAY DIFFRACTION95
1.6713-1.91310.20881540.16397704X-RAY DIFFRACTION96
1.9131-2.41010.161590.15697843X-RAY DIFFRACTION97
2.4101-28.680.16241600.15097988X-RAY DIFFRACTION98

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