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- PDB-3um3: Crystal structure of the Brox Bro1 domain in complex with the C-t... -

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Basic information

Entry
Database: PDB / ID: 3um3
TitleCrystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP4B
Components
  • BRO1 domain-containing protein BROX
  • Charged multivesicular body protein 4b
KeywordsMEMBRANE PROTEIN/TRANSPORT PROTEIN / alpha-helix of C-terminal tail of CHMP4B / ESCRT-III / CHMPs / MEMBRANE PROTEIN-TRANSPORT PROTEIN complex / BROX
Function / homology
Function and homology information


ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / viral budding / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway ...ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / viral budding / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / post-translational protein targeting to endoplasmic reticulum membrane / mitotic nuclear membrane reassembly / regulation of centrosome duplication / nuclear membrane reassembly / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane coat / 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / nervous system process / exit from mitosis / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / mitotic cytokinesis / autophagosome membrane / protein polymerization / autophagosome maturation / Pyroptosis / nuclear pore / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / cytoplasmic side of plasma membrane / nuclear envelope / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / nuclear membrane / vesicle / endosome / regulation of autophagy / cadherin binding / lysosomal membrane / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 4b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 12, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: BRO1 domain-containing protein BROX
B: Charged multivesicular body protein 4b


Theoretical massNumber of molelcules
Total (without water)58,2222
Polymers58,2222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.156, 138.156, 373.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 46521.863 Da / Num. of mol.: 1 / 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 4b / Chromatin-modifying protein 4b / CHMP4b / SNF7 homolog associated with Alix 1 / SNF7-2 / hSnf7-2 / ...Chromatin-modifying protein 4b / CHMP4b / SNF7 homolog associated with Alix 1 / SNF7-2 / hSnf7-2 / Vacuolar protein sorting-associated protein 32-2 / Vps32-2 / hVps32-2


Mass: 11699.792 Da / Num. of mol.: 1 / Fragment: C-terminal tail of CHMP4B 121-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf178, CHMP4B, SHAX1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H444

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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

Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.0M sodium citrate, 0.1M imidazol, 15% glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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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: Apr 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 21693 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 145 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.3refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R9M

3r9m


Resolution: 3.8→48.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5336689.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2144 9.9 %RANDOM
Rwork0.233 ---
all0.233 21693 --
obs0.233 21556 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2265 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 83.3 Å2
Baniso -1Baniso -2Baniso -3
1-19.87 Å20 Å20 Å2
2--19.87 Å20 Å2
3----39.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.93 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 3.8→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 0 3154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.42
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 334 9.8 %
Rwork0.339 3074 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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