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- PDB-5wa1: CHMP4C A232T in complex with ALIX BRO1 -

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Basic information

Entry
Database: PDB / ID: 5wa1
TitleCHMP4C A232T in complex with ALIX BRO1
Components
  • Charged multivesicular body protein 4c
  • Programmed cell death 6-interacting protein
KeywordsCELL CYCLE / cell 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 / vesicle fusion with vacuole / extracellular exosome biogenesis / 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 / Sealing of the nuclear envelope (NE) by ESCRT-III / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / bicellular tight junction assembly / 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 / nucleus organization / RIPK1-mediated regulated necrosis / Macroautophagy / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / bicellular tight junction / Pyroptosis / endoplasmic reticulum exit site / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / protein homooligomerization / Budding and maturation of HIV virion / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / 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: 1.868 Å
AuthorsWenzel, D.M. / Alam, S.L. / Sundquist, W.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112080 United States
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
DepositionJun 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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)44,7582
Polymers44,7582
Non-polymers00
Water1,65792
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 area1110 Å2
ΔGint-11 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.979, 61.450, 76.187
Angle α, β, γ (deg.)90.00, 121.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

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


Mass: 42636.660 Da / Num. of mol.: 1 / Fragment: Bro1 domain (UNP residues 1-358) / Mutation: A232T
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: 2121.218 Da / Num. of mol.: 1 / Fragment: UNP residues 216-233 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CF2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG8000, 100 mM MES, pH 6.5, 200 mM sodium acetate

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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: 1.868→37.811 Å / Num. obs: 38802 / % possible obs: 97.63 % / Redundancy: 2 % / Biso Wilson estimate: 40.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0222 / Net I/σ(I): 8.78
Reflection shellResolution: 1.868→1.935 Å / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 3744 / CC1/2: 0.6 / % possible all: 93.38

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3R

3c3r


Resolution: 1.868→37.811 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30
RfactorNum. reflection% reflection
Rfree0.215 1993 5.16 %
Rwork0.1935 --
obs0.1946 38618 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.868→37.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 0 92 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052971
X-RAY DIFFRACTIONf_angle_d0.7174010
X-RAY DIFFRACTIONf_dihedral_angle_d17.9541107
X-RAY DIFFRACTIONf_chiral_restr0.044452
X-RAY DIFFRACTIONf_plane_restr0.004517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8679-1.91460.40791300.40012390X-RAY DIFFRACTION90
1.9146-1.96640.38941410.36092607X-RAY DIFFRACTION98
1.9664-2.02420.32611410.3132578X-RAY DIFFRACTION97
2.0242-2.08960.33361420.29952591X-RAY DIFFRACTION97
2.0896-2.16430.29391450.26392664X-RAY DIFFRACTION99
2.1643-2.25090.27251430.23182633X-RAY DIFFRACTION99
2.2509-2.35330.23331420.22262624X-RAY DIFFRACTION98
2.3533-2.47740.22951420.21122608X-RAY DIFFRACTION98
2.4774-2.63260.25431440.21212627X-RAY DIFFRACTION98
2.6326-2.83580.24591440.21172661X-RAY DIFFRACTION99
2.8358-3.1210.24111430.20732623X-RAY DIFFRACTION98
3.121-3.57230.24441440.19482648X-RAY DIFFRACTION98
3.5723-4.49960.17361450.15792670X-RAY DIFFRACTION99
4.4996-37.81870.16031470.15572701X-RAY DIFFRACTION98

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