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- PDB-2xs1: Crystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL... -

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Basic information

Entry
Database: PDB / ID: 2xs1
TitleCrystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL Late Domain
Components
  • GAG POLYPROTEIN
  • PROGRAMMED CELL DEATH 6-INTERACTING PROTEIN
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 / 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 / endoplasmic reticulum exit site / Uptake and function of anthrax toxins / immunological synapse / mitotic cytokinesis / bicellular tight junction / viral process / 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 / focal adhesion / centrosome / apoptotic process / host cell nucleus / host cell plasma membrane / structural molecule activity / protein homodimerization activity / RNA binding / zinc ion binding / extracellular exosome / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / 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. ...alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / 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 / Retroviral nucleocapsid Gag protein p24, N-terminal / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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 / 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: 2.296 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: GAG POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)81,2592
Polymers81,2592
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10.6 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.281, 99.271, 72.521
Angle α, β, γ (deg.)90.00, 106.62, 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 GAG POLYPROTEIN / SIVMAC239 GAG P6


Mass: 2422.731 Da / Num. of mol.: 1 / Fragment: RESIDUES 483-502 / Source method: obtained synthetically / Source: (synth.) SIMIAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q76V78, UniProt: P05893*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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 detailsGAG POLYPROTEIN FRAGMENT FROM SIV IS GENBANK ACCESSION M33262

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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: 6.2 / Details: 6.5% PEG4000, 0.2 MGCL2, 0.1M MES PH 6.2

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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: 2.3→45 Å / Num. obs: 44063 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 47.27 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.9 / % possible all: 82.6

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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: 2.296→35.44 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2152 5 %
Rwork0.2051 --
obs0.2075 42967 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.269 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.8666 Å20 Å2-15.4568 Å2
2--3.7809 Å2-0 Å2
3---7.0856 Å2
Refinement stepCycle: LAST / Resolution: 2.296→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 0 58 5672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075700
X-RAY DIFFRACTIONf_angle_d0.9947700
X-RAY DIFFRACTIONf_dihedral_angle_d18.2832143
X-RAY DIFFRACTIONf_chiral_restr0.068884
X-RAY DIFFRACTIONf_plane_restr0.0041005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2964-2.34980.32471060.26012183X-RAY DIFFRACTION78
2.3498-2.40850.30241270.23442508X-RAY DIFFRACTION90
2.4085-2.47360.29731610.23472667X-RAY DIFFRACTION97
2.4736-2.54640.28731330.22852765X-RAY DIFFRACTION99
2.5464-2.62850.29191530.22312775X-RAY DIFFRACTION100
2.6285-2.72250.31761330.22382767X-RAY DIFFRACTION100
2.7225-2.83140.27051390.23152795X-RAY DIFFRACTION100
2.8314-2.96020.29731460.23122776X-RAY DIFFRACTION100
2.9602-3.11620.28321570.22692785X-RAY DIFFRACTION100
3.1162-3.31130.34361330.22872801X-RAY DIFFRACTION100
3.3113-3.56680.26521380.22022806X-RAY DIFFRACTION100
3.5668-3.92530.20951430.18662792X-RAY DIFFRACTION100
3.9253-4.49230.21381630.1692795X-RAY DIFFRACTION100
4.4923-5.65610.20711400.17782806X-RAY DIFFRACTION100
5.6561-35.44470.23061800.18262794X-RAY DIFFRACTION98
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)
10.1136-0.0731-0.0820.97960.67870.26-0.4139-0.23410.6602-0.21550.35151.0395-0.4256-0.03080.00280.693-0.0961-0.14880.40310.27330.8669-15.2015-19.92-32.3252
20.0310.1017-0.0094-0.0350.0162-0.0769-0.48720.50160.9226-0.02130.6361.5445-0.6795-0.445-0.00040.67050.118-0.52460.98330.50662.2425-42.2962-20.9554-35.3098
30.81790.3688-0.31720.7211-0.87970.5987-0.02320.32530.76560.19630.25770.9317-0.1643-0.2894-0.00010.48730.0591-0.18980.56340.25821.0709-28.0572-24.5247-32.0611
44.21350.14730.66713.7037-1.33040.9479-0.11940.43460.2099-0.50960.31630.70290.10120.0126-0.00010.407-0.03650.0350.37750.08210.256-9.9908-30.4815-27.8077
54.15221.51111.67322.4253-0.58242.42680.07450.3006-0.15090.0941-0.2055-0.2167-0.18420.4591-0.00030.29350.00110.14050.3801-0.03430.10914.3937-36.2995-18.1668
60.58860.7325-0.15950.88690.05850.9344-0.0961-0.07730.6435-0.21210.21610.94640.1894-0.7120.00080.2943-0.0383-0.06840.60580.23150.9553-30.4927-35.3065-27.7039
71.0611-1.00970.25661.3383-1.01151.39240.4156-0.3287-0.2120.1629-0.1679-0.28120.4255-0.02740.00010.5574-0.1301-0.17930.43530.20910.6303-81.6268-49.9685-55.1699
8-0.46661.01830.79852.8802-0.09640.81560.38460.2704-0.7980.4247-0.0516-0.72680.00370.16840.00030.426-0.03840.09720.3594-0.08370.5615-58.6284-10.7852-60.2226
90.3370.01440.70551.80660.15890.7775-0.14240.33670.506-0.40990.45280.38110.1227-0.122400.4313-0.0826-0.03550.38690.10190.6194-83.9978-37.2149-64.2331
100.4702-0.0087-0.4668-0.03270.13410.18170.3758-1.5239-0.97420.14420.39371.22640.5803-1.03680.0021.0337-0.174-0.70370.64810.4721.4749-89.0573-65.2615-54.7131
110.95110.3342-0.16011.0152-0.67430.48090.32630.0275-0.36150.1972-0.1044-0.30020.46550.18220.00010.73410.0612-0.46320.49330.05921.0811-67.5879-55.5248-49.3136
120.6250.3475-0.32610.9121-1.1590.84010.5995-0.3491-0.85670.6948-0.2369-0.8040.0581-0.00920.00090.4483-0.0951-0.07160.32870.0240.5073-73.7855-31.2822-56.9007
13-0.06720.03560.00630.058-0.05460.08690.58070.2885-0.4744-0.3919-0.3178-1.2439-0.07150.02520.00040.7451-0.1551-0.22760.46160.07571.3482-64.1404-34.874-58.0938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:17)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:51)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 52:91)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 92:227)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 228:332)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 333:369)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 370:431)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 432:490)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 491:540)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 541:564)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 565:647)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 648:698)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 42:56)

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