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- PDB-2r05: Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL L... -

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Basic information

Entry
Database: PDB / ID: 2r05
TitleCrystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain
Components
  • Programmed cell death 6-interacting protein
  • p6-Gag
KeywordsAPOPTOSIS / coiled-coil / Cytoplasm / Host-virus interaction / Polymorphism / Protein transport / Transport / AIDS / Capsid protein / Lipoprotein / Membrane / Metal-binding / Myristate / Nucleus / Phosphorylation / RNA-binding / Viral nucleoprotein / Virion / Zinc / Zinc-finger
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 / bicellular tight junction assembly / multivesicular body sorting pathway / 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 / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / bicellular tight junction / macroautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / host multivesicular body / calcium-dependent protein binding / melanosome / extracellular vesicle / protein transport / viral nucleocapsid / endosome / viral translational frameshifting / focal adhesion / centrosome / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Gag protein p6 / Gag protein p6 / 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 / 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 / Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsHill, C.P. / Zhai, Q. / Fisher, R.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV.
Authors: Zhai, Q. / Fisher, R.D. / Chung, H.Y. / Myszka, D.G. / Sundquist, W.I. / Hill, C.P.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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: p6-Gag


Theoretical massNumber of molelcules
Total (without water)79,3372
Polymers79,3372
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.090, 99.440, 73.543
Angle α, β, γ (deg.)90.000, 107.290, 90.000
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: 78074.664 Da / Num. of mol.: 1 / Fragment: ALIX Bro1-V domains / Mutation: K268Y,K269Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ RIL / References: UniProt: Q8WUM4
#2: Protein/peptide p6-Gag


Mass: 1262.476 Da / Num. of mol.: 1 / Fragment: UNP residues 482-492 / Source method: obtained synthetically
Details: The sequence of this peptide naturally exists in Human immunodeficiency virus type 1(HIV-1).
References: UniProt: P35962
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 32602 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.126 / Χ2: 1.118 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.55-2.645.50.36632771.0699.5
2.64-2.755.70.29532741.052100
2.75-2.875.80.21933001.09100
2.87-3.025.80.17332761.102100
3.02-3.215.80.13833041.137100
3.21-3.465.80.1132971.115100
3.46-3.815.80.0932851.021100
3.81-4.365.80.09733271.128100
4.36-5.495.70.13333041.21999.8
5.49-405.40.14129581.27987.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.55→27.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 23.562 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.477 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1611 5 %RANDOM
Rwork0.225 ---
obs0.228 32396 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.238 Å2
Baniso -1Baniso -2Baniso -3
1--7.48 Å20 Å2-6.08 Å2
2--0.09 Å20 Å2
3---3.78 Å2
Refinement stepCycle: LAST / Resolution: 2.55→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 0 17 5591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225659
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9767645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7825.451266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.109151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7041530
X-RAY DIFFRACTIONr_chiral_restr0.0970.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024219
X-RAY DIFFRACTIONr_nbd_refined0.2160.22435
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.27
X-RAY DIFFRACTIONr_mcbond_it0.6041.53644
X-RAY DIFFRACTIONr_mcangle_it1.04525695
X-RAY DIFFRACTIONr_scbond_it1.54932244
X-RAY DIFFRACTIONr_scangle_it2.4134.51950
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 101 -
Rwork0.29 2309 -
all-2410 -
obs--99.5 %
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)
12.9273-1.14220.76672.7298-0.9423.181-0.1690.53921.4192-0.31520.1821.2356-0.4319-0.9542-0.0130.01940.1371-0.09860.22210.23350.6284-32.9678-20.4479-34.4244
25.55991.5369-1.04185.5197-0.67435.8274-0.22050.50820.5696-0.61570.07940.6682-0.1604-0.07170.14110.17580.0845-0.09870.23780.22070.3986-22.6133-23.9032-36.8869
33.8553-0.41411.07351.4999-0.57831.40850.05420.1170.0223-0.07430.0310.13660.0093-0.0351-0.08520.3413-0.01320.10870.33780.02750.1918-0.9237-33.8505-23.3465
45.7487-0.2922.11481.7128-0.87611.68210.0772-0.297-0.15840.03290.05790.1657-0.0141-0.1267-0.13510.36640.01410.16230.3289-0.01980.189-1.727-36.3948-19.396
55.96631.13562.92322.59950.01943.81620.66310.0013-0.4820.2662-0.1335-0.13790.53620.1317-0.52970.3177-0.077-0.14350.16320.17170.2424-79.8019-51.2075-55.5551
68.53859.99670.720412.0780.33330.75650.22350.1135-0.28220.0230.135-0.2099-0.02270.0563-0.35850.1618-0.010.14110.1929-0.08760.3546-62.6182-16.9447-61.1143
74.48540.51612.07331.2855-0.19272.25360.4827-0.1987-0.5812-0.0051-0.0023-0.08680.619-0.0919-0.48040.3062-0.0354-0.2130.13950.12540.3727-76.7513-55.2397-53.2044
810.419510.18933.26911.23792.62881.96410.6601-0.4473-0.41690.4934-0.1995-0.5331-0.0389-0.0989-0.46060.2578-0.06390.01320.16580.03210.3334-74.0723-31.8188-57.4139
912.1121-18.7725.890229.0939-9.1292.8645-2.5586-4.1147-1.80983.56830.6065-1.06030.0765-1.13311.9520.6607-0.00360.00530.64890.00410.6593-63.6858-33.7358-56.8205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 541 - 53
2X-RAY DIFFRACTION2AA55 - 11754 - 116
3X-RAY DIFFRACTION3AA118 - 291117 - 290
4X-RAY DIFFRACTION4AA292 - 367291 - 366
5X-RAY DIFFRACTION5AA368 - 425367 - 424
6X-RAY DIFFRACTION6AA426 - 513425 - 512
7X-RAY DIFFRACTION7AA514 - 646513 - 645
8X-RAY DIFFRACTION8AA647 - 698646 - 697
9X-RAY DIFFRACTION9BB34 - 441 - 11

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