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- PDB-1zb1: Structure basis for endosomal targeting by the Bro1 domain -

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Basic information

Entry
Database: PDB / ID: 1zb1
TitleStructure basis for endosomal targeting by the Bro1 domain
ComponentsBRO1 protein
KeywordsPROTEIN TRANSPORT / Bro1 / Aip1 / Bro1 domain / Snf7 / Trafficking
Function / homology
Function and homology information


positive regulation of protein deubiquitination / intralumenal vesicle formation / mitochondria-associated ubiquitin-dependent protein catabolic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vacuolar transport / deubiquitinase activator activity / protein deubiquitination ...positive regulation of protein deubiquitination / intralumenal vesicle formation / mitochondria-associated ubiquitin-dependent protein catabolic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / ATP export / vacuolar transport / deubiquitinase activator activity / protein deubiquitination / extracellular vesicle / ubiquitin-dependent protein catabolic process / endosome membrane / endosome / cytosol / cytoplasm
Similarity search - Function
alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar-sorting protein BRO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKim, J. / Sitaraman, S. / Hierro, A. / Beach, B.M. / Odorizzi, G. / Hurley, J.H.
CitationJournal: Dev.Cell / Year: 2005
Title: Structural basis for endosomal targeting by the Bro1 domain.
Authors: Kim, J. / Sitaraman, S. / Hierro, A. / Beach, B.M. / Odorizzi, G. / Hurley, J.H.
History
DepositionApr 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRO1 protein
B: BRO1 protein


Theoretical massNumber of molelcules
Total (without water)91,2152
Polymers91,2152
Non-polymers00
Water8,071448
1
A: BRO1 protein


Theoretical massNumber of molelcules
Total (without water)45,6081
Polymers45,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRO1 protein


Theoretical massNumber of molelcules
Total (without water)45,6081
Polymers45,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.445, 58.274, 120.823
Angle α, β, γ (deg.)90.00, 90.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BRO1 protein


Mass: 45607.578 Da / Num. of mol.: 2 / Fragment: Bro1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGST-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P48582
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG 3350, tri-potassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9796,0.9790,0.9720
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.9791
30.9721
ReflectionResolution: 1.95→40.3 Å / Num. all: 72861 / Num. obs: 77077
Reflection shellResolution: 1.95→2.02 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.95→40.26 Å / σ(F): 3
RfactorNum. reflection
Rfree0.252 7245
Rwork0.224 -
all-71482
obs-71482
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 0 448 6490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.1

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