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- PDB-4jjy: Alix V domain -

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Basic information

Entry
Database: PDB / ID: 4jjy
TitleAlix V domain
ComponentsProgrammed cell death 6-interacting protein
KeywordsPROTEIN BINDING / Ubiquitin / Endosome / Membrane Trafficking / virus budding / ESCRTI
Function / homology
Function and homology information


proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / regulation of centrosome duplication ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / regulation of centrosome duplication / midbody abscission / multivesicular body sorting pathway / bicellular tight junction assembly / actomyosin / positive regulation of exosomal secretion / multivesicular body assembly / Flemming body / RIPK1-mediated regulated necrosis / viral budding via host ESCRT complex / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / bicellular tight junction / endoplasmic reticulum exit site / macroautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / endosome / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 6.503 Å
AuthorsPashkova, N. / Gakhar, L. / Yu, L. / Piper, R.C.
CitationJournal: Dev.Cell / Year: 2013
Title: The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes.
Authors: Pashkova, N. / Gakhar, L. / Winistorfer, S.C. / Sunshine, A.B. / Rich, M. / Dunham, M.J. / Yu, L. / Piper, R.C.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death 6-interacting protein
B: Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)81,7972
Polymers81,7972
Non-polymers00
Water0
1
A: Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)40,8981
Polymers40,8981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death 6-interacting protein


Theoretical massNumber of molelcules
Total (without water)40,8981
Polymers40,8981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.770, 223.770, 223.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 40898.375 Da / Num. of mol.: 2
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

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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: 5.71 Å3/Da / Density % sol: 78.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.976 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: Rosenbaum-Rock monochromator double crystal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 6.5→39.56 Å / Num. all: 3774 / Num. obs: 3774 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 21.41 % / Biso Wilson estimate: 468.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.3
Reflection shellResolution: 6.5→6.73 Å / Redundancy: 22.27 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.1 / Num. unique all: 370 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 6.503→39.557 Å / SU ML: 1.09 / σ(F): 0 / Phase error: 33.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2832 377 10.03 %RANDOM
Rwork0.2028 ---
obs0.2107 3760 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.503→39.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5396 0 0 0 5396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025452
X-RAY DIFFRACTIONf_angle_d0.557358
X-RAY DIFFRACTIONf_dihedral_angle_d8.9982118
X-RAY DIFFRACTIONf_chiral_restr0.031864
X-RAY DIFFRACTIONf_plane_restr0.003972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5032-7.43880.38291250.2861112X-RAY DIFFRACTION100
7.4388-9.35160.32351240.23921122X-RAY DIFFRACTION100
9.3516-39.5580.25151280.17571149X-RAY DIFFRACTION99

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