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- PDB-3um1: Crystal structure of the Brox Bro1 domain in complex with the C-t... -

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Basic information

Entry
Database: PDB / ID: 3um1
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 hairpin / 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 assembly / multivesicular body membrane / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / nuclear pore / multivesicular body / 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: 2.708 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 1.3Nov 6, 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
D: BRO1 domain-containing protein BROX
E: Charged multivesicular body protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7485
Polymers99,6564
Non-polymers921
Water2,828157
1
A: BRO1 domain-containing protein BROX
B: Charged multivesicular body protein 5
hetero molecules

D: BRO1 domain-containing protein BROX
E: Charged multivesicular body protein 5


Theoretical massNumber of molelcules
Total (without water)99,7485
Polymers99,6564
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3720 Å2
ΔGint-29 kcal/mol
Surface area35740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.920, 111.390, 116.270
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 BRO1 domain-containing protein BROX / BRO1 domain- and CAAX motif-containing protein


Mass: 42533.410 Da / Num. of mol.: 2 / Fragment: Brox bro1 domain 2-377
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 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: 7294.708 Da / Num. of mol.: 2 / Fragment: C-terminal tail of CHMP5 151-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: C9orf83, CGI-34, CHMP5, HSPC177, PNAS-114, PNAS-2, SNF7DC2
Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 157 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
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: 2.7→50 Å / Num. obs: 23032 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.1

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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: 2.708→43.319 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1073 4.97 %RANDOM
Rwork0.1862 ---
all0.1895 23032 --
obs0.1895 21584 86.21 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.133 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.9683 Å2-0 Å20 Å2
2---2.2001 Å20 Å2
3---3.1685 Å2
Refinement stepCycle: LAST / Resolution: 2.708→43.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 6 157 6401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056397
X-RAY DIFFRACTIONf_angle_d0.8958659
X-RAY DIFFRACTIONf_dihedral_angle_d14.7142362
X-RAY DIFFRACTIONf_chiral_restr0.07944
X-RAY DIFFRACTIONf_plane_restr0.0041110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7081-2.83130.30891240.24552326X-RAY DIFFRACTION80
2.8313-2.98060.29421250.23012477X-RAY DIFFRACTION84
2.9806-3.16720.33251290.22212511X-RAY DIFFRACTION86
3.1672-3.41170.2631320.1972583X-RAY DIFFRACTION88
3.4117-3.75490.29431400.17492621X-RAY DIFFRACTION89
3.7549-4.29780.22061430.15132649X-RAY DIFFRACTION89
4.2978-5.41310.19511300.15662676X-RAY DIFFRACTION89
5.4131-43.32410.22631500.19752668X-RAY DIFFRACTION85

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