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- PDB-3um0: Crystal structure of the Brox Bro1 domain in complex with the C-t... -

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Basic information

Entry
Database: PDB / ID: 3um0
TitleCrystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5
Components
  • BRO1 domain-containing protein BROX
  • Charged multivesicular body protein 5
KeywordsMEMBRANE PROTEIN/TRANSPORT PROTEIN / beta hairpins / ESCRT-III / CHMPs / MEMBRANE PROTEIN-TRANSPORT PROTEIN complex / BROX
Function / homology
Function and homology information


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 / late endosome to vacuole transport via multivesicular body sorting pathway / cellular response to muramyl dipeptide ...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 / late endosome to vacuole transport via multivesicular body sorting pathway / cellular response to muramyl dipeptide / mitotic nuclear membrane reassembly / regulation of centrosome duplication / nuclear membrane reassembly / multivesicular body sorting pathway / vesicle budding from membrane / midbody abscission / membrane fission / plasma membrane repair / 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 / Budding and maturation of HIV virion / kinetochore / autophagy / nuclear envelope / protein transport / cellular response to lipopolysaccharide / midbody / nuclear membrane / cadherin binding / lysosomal membrane / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
BRO1 domain-containing protein BROX / alix/aip1 like domains / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...BRO1 domain-containing protein BROX / alix/aip1 like domains / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
BRO1 domain-containing protein BROX / Charged multivesicular body protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsJiang, J.S. / Mu, R.L. / Xiao, T.
CitationJournal: Structure / Year: 2012
Title: Two Distinct Binding Modes Define the Interaction of Brox with the C-Terminal Tails of CHMP5 and CHMP4B.
Authors: Mu, R. / Dussupt, V. / Jiang, J. / Sette, P. / Rudd, V. / Chuenchor, W. / Bello, N.F. / Bouamr, F. / Xiao, T.S.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRO1 domain-containing protein BROX
B: Charged multivesicular body protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6293
Polymers48,5372
Non-polymers921
Water36020
1
A: BRO1 domain-containing protein BROX
B: Charged multivesicular body protein 5
hetero molecules

A: BRO1 domain-containing protein BROX
B: Charged multivesicular body protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2596
Polymers97,0744
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4060 Å2
ΔGint-28 kcal/mol
Surface area38670 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.260, 46.240, 68.829
Angle α, β, γ (deg.)90.00, 105.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BRO1 domain-containing protein BROX / BRO1 domain- and CAAX motif-containing protein


Mass: 46406.777 Da / Num. of mol.: 1 / Fragment: Brox bro1 domain 2-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BROFTI, BROX, C1orf58 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5VW32
#2: Protein/peptide 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 / Vps60 / hVps60


Mass: 2130.397 Da / Num. of mol.: 1
Fragment: Synthetic peptide of C-terminal tail of CHMP5 200-219
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZZ3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 9731 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R9M

3r9m


Resolution: 3.102→46.514 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 920 10.05 %
Rwork0.1964 --
obs0.2025 9153 93.38 %
all-9731 -
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.436 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.2194 Å2-0 Å2-3.9365 Å2
2---0.7157 Å2-0 Å2
3----22.5037 Å2
Refinement stepCycle: LAST / Resolution: 3.102→46.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 6 20 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073328
X-RAY DIFFRACTIONf_angle_d1.1084503
X-RAY DIFFRACTIONf_dihedral_angle_d15.8791243
X-RAY DIFFRACTIONf_chiral_restr0.076489
X-RAY DIFFRACTIONf_plane_restr0.007578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1023-3.26580.33341120.2756973X-RAY DIFFRACTION79
3.2658-3.47030.34841220.25241113X-RAY DIFFRACTION89
3.4703-3.73820.29881300.2171161X-RAY DIFFRACTION94
3.7382-4.11420.27411330.18621202X-RAY DIFFRACTION95
4.1142-4.7090.22641370.15771231X-RAY DIFFRACTION98
4.709-5.93090.23821410.19021247X-RAY DIFFRACTION99
5.9309-46.51910.22151450.18921306X-RAY DIFFRACTION99

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