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- PDB-3c3q: ALIX Bro1-domain:CHMIP4B co-crystal structure -

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Basic information

Entry
Database: PDB / ID: 3c3q
TitleALIX Bro1-domain:CHMIP4B co-crystal structure
Components
  • Charged multivesicular body protein 4b peptide
  • Programmed cell death 6-interacting protein
KeywordsTRANSPORT PROTEIN / ALIX CHMP4B BRO1 amphipathic-helix / Cataract / Disease mutation / Protein transport / Transport / Apoptosis / Host-virus interaction
Function / homology
Function and homology information


proteinase activated receptor binding / actomyosin contractile ring assembly / regulation of extracellular exosome assembly / maintenance of lens transparency / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / multivesicular body-lysosome fusion / amphisome membrane ...proteinase activated receptor binding / actomyosin contractile ring assembly / regulation of extracellular exosome assembly / maintenance of lens transparency / extracellular exosome biogenesis / viral budding / maintenance of epithelial cell apical/basal polarity / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / positive regulation of extracellular exosome assembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of membrane permeability / post-translational protein targeting to endoplasmic reticulum membrane / nuclear membrane reassembly / membrane coat / multivesicular body sorting pathway / bicellular tight junction assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / regulation of centrosome duplication / membrane fission / positive regulation of exosomal secretion / actomyosin / vesicle budding from membrane / multivesicular body assembly / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / plasma membrane repair / exit from mitosis / Flemming body / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / nervous system process / RIPK1-mediated regulated necrosis / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / mitotic cytokinesis / autophagosome membrane / endoplasmic reticulum exit site / Uptake and function of anthrax toxins / immunological synapse / protein polymerization / Pyroptosis / bicellular tight junction / autophagosome maturation / 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 / protein homooligomerization / kinetochore / Regulation of necroptotic cell death / autophagy / cytoplasmic side of plasma membrane / calcium-dependent protein binding / melanosome / nuclear envelope / protein transport / extracellular vesicle / midbody / Translation of Replicase and Assembly of the Replication Transcription Complex / vesicle / endosome / cadherin binding / lysosomal membrane / focal adhesion / apoptotic process / centrosome / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
alix/aip1 like domains / 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 ...alix/aip1 like domains / 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 4b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMcCullough, J.B. / Fisher, R.D. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: ALIX-CHMP4 interactions in the human ESCRT pathway.
Authors: McCullough, J. / Fisher, R.D. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 4b peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9863
Polymers44,8942
Non-polymers921
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.515, 62.586, 76.053
Angle α, β, γ (deg.)90.00, 121.51, 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 / Hp95


Mass: 42735.789 Da / Num. of mol.: 1 / Fragment: BRO1 domain (UNP residues 1-359)
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 4b peptide / Chromatin-modifying protein 4b / CHMP4b / Vacuolar protein-sorting-associated protein 7-2 / SNF7- 2 ...Chromatin-modifying protein 4b / CHMP4b / Vacuolar protein-sorting-associated protein 7-2 / SNF7- 2 / hSnf7-2 / SNF7 homolog associated with Alix 1 / hVps32


Mass: 2158.277 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHMP4B peptide chemically synthesized. This sequence is found naturally in Homo sapiens (humans).
References: UniProt: Q9H444
#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.: 90 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2008 / Details: VARIMAX-HR Confocal Optic
RadiationMonochromator: Copper anode, varimax confocal optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26458 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 67.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→36.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.881 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29024 1899 7.2 %RANDOM
Rwork0.22801 ---
all0.23238 ---
obs0.23238 24386 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.926 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20.25 Å2
2--3.35 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 6 90 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9594060
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7445373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11625.435138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.63515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.291511
X-RAY DIFFRACTIONr_chiral_restr0.120.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022249
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22047
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.51937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57623002
X-RAY DIFFRACTIONr_scbond_it2.17831221
X-RAY DIFFRACTIONr_scangle_it3.314.51058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 93 -
Rwork0.326 1325 -
obs--68.11 %

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