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- PDB-3uly: Crystal Structure of BROX Bro1 Domain in Complex with the C-Termi... -

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Basic information

Entry
Database: PDB / ID: 3uly
TitleCrystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails 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


multivesicular body-lysosome fusion / amphisome membrane / viral budding / 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 / regulation of centrosome duplication ...multivesicular body-lysosome fusion / amphisome membrane / viral budding / 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 / regulation of centrosome duplication / mitotic nuclear membrane reassembly / nuclear membrane reassembly / cellular response to muramyl dipeptide / midbody abscission / multivesicular body sorting pathway / plasma membrane repair / membrane fission / vesicle budding from membrane / 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 / autophagosome maturation / regulation of receptor recycling / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / erythrocyte differentiation / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / nuclear envelope / midbody / cellular response to lipopolysaccharide / 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: 2.6 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)53,7943
Polymers53,7012
Non-polymers921
Water1,51384
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)107,5876
Polymers107,4034
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3880 Å2
ΔGint-30 kcal/mol
Surface area36650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.377, 46.033, 68.557
Angle α, β, γ (deg.)90.00, 104.52, 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 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.: 1 / Fragment: C-terminal tails 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.: 84 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
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: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15918 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.7

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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: 2.6→41.72 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 742 5.04 %
Rwork0.166 --
obs0.169 14719 90.1 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.61 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.3622 Å2-0 Å2-7.3996 Å2
2--2.1594 Å2-0 Å2
3----16.5216 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 6 84 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053321
X-RAY DIFFRACTIONf_angle_d0.9694491
X-RAY DIFFRACTIONf_dihedral_angle_d14.7681239
X-RAY DIFFRACTIONf_chiral_restr0.069488
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6017-2.80250.31791070.23992176X-RAY DIFFRACTION71
2.8025-3.08450.24171340.20682678X-RAY DIFFRACTION86
3.0845-3.53060.26491610.16912921X-RAY DIFFRACTION96
3.5306-4.44740.16551760.13363038X-RAY DIFFRACTION98
4.4474-41.72320.20061640.16473164X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.2706 Å / Origin y: -10.4393 Å / Origin z: 3.5971 Å
111213212223313233
T0.1747 Å20.0519 Å20.0315 Å2-0.1624 Å2-0.0151 Å2--0.1721 Å2
L1.0097 °20.4577 °20.6139 °2-0.6402 °20.6753 °2--1.7986 °2
S-0.0625 Å °0.2373 Å °-0.0216 Å °-0.1918 Å °0.0829 Å °-0.031 Å °-0.3048 Å °-0.0407 Å °-0.0118 Å °
Refinement TLS groupSelection details: all

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