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- PDB-5v3r: CHMP4C in complex with ALIX BRO1 -

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Basic information

Entry
Database: PDB / ID: 5v3r
TitleCHMP4C in complex with ALIX BRO1
Components
  • Charged multivesicular body protein 4c
  • Programmed cell death 6-interacting protein
KeywordsCELL DIVISION / TRANSPORT PROTEIN / abscission checkpoint
Function / homology
Function and homology information


proteinase activated receptor binding / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / abscission / amphisome membrane / multivesicular body-lysosome fusion / viral budding ...proteinase activated receptor binding / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / abscission / amphisome membrane / multivesicular body-lysosome fusion / viral budding / extracellular exosome biogenesis / vesicle fusion with vacuole / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / regulation of membrane permeability / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / bicellular tight junction assembly / vesicle budding from membrane / actomyosin / membrane fission / plasma membrane repair / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Flemming body / RIPK1-mediated regulated necrosis / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / endoplasmic reticulum exit site / autophagosome membrane / Uptake and function of anthrax toxins / autophagosome maturation / immunological synapse / mitotic cytokinesis / bicellular tight junction / Pyroptosis / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / kinetochore / autophagy / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / endosome / lysosomal membrane / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Snf7 family ...alix/aip1 like domains / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / 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
Programmed cell death 6-interacting protein / Charged multivesicular body protein 4c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.906 Å
AuthorsWenzel, D.M. / Alam, S.L. / Sundquist, W.I.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: A cancer-associated polymorphism in ESCRT-III disrupts the abscission checkpoint and promotes genome instability.
Authors: Sadler, J.B.A. / Wenzel, D.M. / Williams, L.K. / Guindo-Martinez, M. / Alam, S.L. / Mercader, J.M. / Torrents, D. / Ullman, K.S. / Sundquist, W.I. / Martin-Serrano, J.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 6-interacting protein
B: Charged multivesicular body protein 4c


Theoretical massNumber of molelcules
Total (without water)44,7542
Polymers44,7542
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization binding experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-10 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.590, 60.775, 75.654
Angle α, β, γ (deg.)90.00, 121.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / ALG-2-interacting protein X / Hp95 / ALIX BRO1


Mass: 42662.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUM4
#2: Protein/peptide Charged multivesicular body protein 4c / Chromatin-modifying protein 4c / CHMP4c / SNF7 homolog associated with Alix 3 / SNF7-3 / hSnf7-3 / ...Chromatin-modifying protein 4c / CHMP4c / SNF7 homolog associated with Alix 3 / SNF7-3 / hSnf7-3 / Vacuolar protein sorting-associated protein 32-3 / hVps32-3


Mass: 2091.192 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 216-233) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CF2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG20000, 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.906→36.18 Å / Num. obs: 35304 / % possible obs: 96.04 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.01955 / Net I/av σ(I): 10.17 / Net I/σ(I): 10.17
Reflection shellResolution: 1.906→1.974 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5925 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 2927 / CC1/2: 0.702 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C3R

3c3r


Resolution: 1.906→36.18 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.45
RfactorNum. reflection% reflection
Rfree0.2131 1987 5.66 %
Rwork0.193 --
obs0.1942 35118 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.906→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 0 99 3006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072961
X-RAY DIFFRACTIONf_angle_d0.8173997
X-RAY DIFFRACTIONf_dihedral_angle_d21.2141102
X-RAY DIFFRACTIONf_chiral_restr0.047450
X-RAY DIFFRACTIONf_plane_restr0.005516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9061-1.95380.40291060.37561733X-RAY DIFFRACTION71
1.9538-2.00660.27081390.30292354X-RAY DIFFRACTION97
2.0066-2.06570.30861460.27152414X-RAY DIFFRACTION98
2.0657-2.13230.2511450.24932398X-RAY DIFFRACTION99
2.1323-2.20850.23921420.21972402X-RAY DIFFRACTION98
2.2085-2.29690.26631420.21592381X-RAY DIFFRACTION97
2.2969-2.40150.2381470.19082441X-RAY DIFFRACTION99
2.4015-2.5280.22551450.20552412X-RAY DIFFRACTION99
2.528-2.68640.23421460.20142424X-RAY DIFFRACTION99
2.6864-2.89370.2321430.20542392X-RAY DIFFRACTION97
2.8937-3.18480.24831450.20522436X-RAY DIFFRACTION99
3.1848-3.64530.22931450.19822411X-RAY DIFFRACTION97
3.6453-4.59140.17411480.16192459X-RAY DIFFRACTION99
4.5914-37.55550.16641480.1642474X-RAY DIFFRACTION97

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