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- PDB-2xs8: Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARK... -

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Basic information

Entry
Database: PDB / ID: 2xs8
TitleCrystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain
Components
  • PROGRAMMED CELL DEATH 6-INTERACTING PROTEIN
  • SIVAGMTAN-1 GAG P6
KeywordsPROTEIN TRANSPORT/VIRAL PROTEIN / PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX / CELL CYCLE
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 / extracellular exosome biogenesis / viral budding / 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 / extracellular exosome biogenesis / viral budding / 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 / endoplasmic reticulum exit site / Uptake and function of anthrax toxins / mitotic cytokinesis / immunological synapse / bicellular tight junction / macroautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / viral nucleocapsid / host cell cytoplasm / endosome / viral translational frameshifting / focal adhesion / centrosome / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / membrane / cytosol
Similarity search - Function
alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. ...alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / alix/aip1 like domains / ALIX V-shaped domain / Vacuolar protein-sorting protein Bro1-like / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / : / gag protein p24 N-terminal domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SIMIAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsZhai, Q. / Landesman, M. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
CitationJournal: J.Virol. / Year: 2011
Title: Identification and Structural Characterization of the Alix-Binding Late Domains of Sivmac239 and Sivagmtan-1.
Authors: Zhai, Q. / Landesman, M. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: SIVAGMTAN-1 GAG P6


Theoretical massNumber of molelcules
Total (without water)80,8342
Polymers80,8342
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-8.3 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.542, 99.076, 72.594
Angle α, β, γ (deg.)90.00, 106.87, 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: 78836.547 Da / Num. of mol.: 1 / Fragment: BRO1-V DOMAINS, RESIDUES 1-698 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET151 TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8WUM4
#2: Protein/peptide SIVAGMTAN-1 GAG P6


Mass: 1997.298 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-41 / Source method: obtained synthetically / Source: (synth.) SIMIAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q02843*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 268 TO TYR ENGINEERED RESIDUE IN CHAIN A, LYS 269 TO TYR
Sequence detailsCHAIN B HAS GENANK ID U58991

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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: 3.19 Å3/Da / Density % sol: 61.4 % / Description: NONE
Crystal growpH: 6.1 / Details: 6.1% PEG4000, 0.2M MGCL2, 0.1M MES PH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 23, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 34197 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 53.09 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.5 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEV

2oev


Resolution: 2.498→41.063 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1626 5 %
Rwork0.2038 --
obs0.2068 32653 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.248 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 86.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.3031 Å20 Å2-16.9969 Å2
2--3.9807 Å20 Å2
3---5.3224 Å2
Refinement stepCycle: LAST / Resolution: 2.498→41.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5559 0 0 22 5581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085644
X-RAY DIFFRACTIONf_angle_d1.0577624
X-RAY DIFFRACTIONf_dihedral_angle_d14.8082142
X-RAY DIFFRACTIONf_chiral_restr0.073875
X-RAY DIFFRACTIONf_plane_restr0.004995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4981-2.57160.416820.29151797X-RAY DIFFRACTION67
2.5716-2.65460.33431170.25322265X-RAY DIFFRACTION84
2.6546-2.74940.33041220.24142588X-RAY DIFFRACTION94
2.7494-2.85950.30881450.23452660X-RAY DIFFRACTION99
2.8595-2.98960.32371360.24242693X-RAY DIFFRACTION100
2.9896-3.14710.28671570.23832712X-RAY DIFFRACTION100
3.1471-3.34420.34711210.23722703X-RAY DIFFRACTION100
3.3442-3.60230.28511360.21562725X-RAY DIFFRACTION100
3.6023-3.96460.25181430.18642729X-RAY DIFFRACTION100
3.9646-4.53760.21011640.16922701X-RAY DIFFRACTION100
4.5376-5.71450.24761280.18022723X-RAY DIFFRACTION100
5.7145-41.06850.22091750.17222731X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3054-0.2307-0.53871.13650.28070.6115-0.64640.19861.4777-0.24020.38251.178-0.7172-0.3251-0.00010.80030.1515-0.22680.69570.48781.5582-34.046-21.4114-35.1347
21.076-0.1043-0.22250.6339-0.40020.3719-0.49210.00850.2833-0.66580.52131.1447-0.8562-0.8180.00060.62840.1089-0.2370.46440.2151.12-28.3602-23.5088-31.9607
33.82630.69990.22352.8499-0.50731.1555-0.16660.360.2248-0.45520.34780.6293-0.1922-0.1579-0.00020.4058-0.00590.07120.30470.13130.2324-9.9842-30.5881-27.7834
45.06371.82421.56863.0541-0.27712.06150.16450.1495-0.30780.1892-0.1997-0.2363-0.18030.4774-0.00060.3221-0.01460.15010.4415-0.02620.148814.2777-36.6416-18.3546
50.90350.47080.43710.14140.1684-0.8048-0.2632-0.02490.9051-0.24410.03290.52850.0006-0.0443-0.00050.4099-0.0252-0.16490.75250.28090.901-40.1353-39.37-34.7413
60.4347-0.65090.16550.62160.04710.87020.4309-0.8392-0.46480.13260.23180.17490.8075-0.162600.6464-0.2344-0.25740.55570.280.7473-90.3086-50.8231-57.3411
7-0.05240.54190.70922.1837-0.28521.22110.1830.1779-0.87520.23110.1239-0.84270.05470.1446-00.468-0.01970.13330.4424-0.1670.6353-58.1871-11.3306-59.974
80.4181-0.18540.74911.23080.20651.23280.10060.59020.5108-0.25840.45990.5753-0.01-0.35260.00050.5297-0.0489-0.080.45150.11180.8155-83.7317-36.465-63.7959
9-0.0026-0.0434-0.01820.00330.05660.00260.39080.0027-0.49250.3494-0.2985-0.87970.4986-0.04780.00061.3377-0.2666-0.7950.74230.50841.3859-96.2665-67.3546-59.2731
100.47940.3716-0.29140.3873-0.78111.41550.4984-0.155-0.6890.2073-0.0114-0.25210.69320.27480.00040.8350.085-0.57560.4130.11251.0893-66.9936-55.7648-47.552
110.34890.05620.04290.18760.04340.05460.18080.2569-0.6542-0.361-0.0809-0.1430.26940.013-0.00030.6153-0.1602-0.28080.53930.24240.7747-89.7739-48.5314-64.0958
120.7165-0.4349-0.04660.3326-0.27990.07780.5338-0.7112-0.7050.4119-0.3256-0.4403-0.00460.353800.8184-0.2921-0.10590.6825-0.06340.7352-62.5864-19.1679-51.9076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:44)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 45:91)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 92:224)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 225:332)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 333:385)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 386:432)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 433:493)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 494:535)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 536:555)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 556:641)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 642:671)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 672:698)

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