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- PDB-2r03: Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain -

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Basic information

Entry
Database: PDB / ID: 2r03
TitleCrystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain
Components
  • Programmed cell death 6-interacting protein
  • p6-Gag
KeywordsAPOPTOSIS / coiled-coil / Cytoplasm / Host-virus interaction / Polymorphism / Protein transport / Transport / Capsid protein / Core protein / Metal-binding / 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 / bicellular tight junction assembly / midbody abscission / actomyosin / multivesicular body sorting pathway / 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 / calcium-dependent protein binding / melanosome / extracellular vesicle / protein transport / viral nucleocapsid / nucleic acid binding / structural constituent of virion / endosome / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / zinc ion binding / membrane / cytosol
Similarity search - Function
alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / Gag protein p15 / Gag protein p15 / 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 ...alix/aip1 in complex with the ypdl late domain / alix/aip1 like domains / Gag protein p15 / Gag protein p15 / 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 / : / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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: 2.59 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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)79,0252
Polymers79,0252
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.383, 98.570, 72.799
Angle α, β, γ (deg.)90.000, 107.070, 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: 950.002 Da / Num. of mol.: 1 / Fragment: UNP residues 456-463 / Source method: obtained synthetically
Details: The seqience of this peptide anturally exists in Human immunodeficiency virus type 1(HIV-1).
References: UniProt: P69732
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
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: 0.97946 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 29646 / % possible obs: 98.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.15 / Χ2: 1.137 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.59-2.692.60.30628881.13596.5
2.69-2.82.90.26829271.07298
2.8-2.9330.22929821.1998.9
2.93-3.083.10.20229961.06399.8
3.08-3.283.10.19330251.26899.8
3.28-3.533.10.17929891.18799.7
3.53-3.883.10.16229811.14999.5
3.88-4.453.10.14930171.12899.5
4.45-5.63.10.14329941.10398.9
5.6-5030.12828471.05892

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementResolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / SU B: 24.481 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.581 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1488 5 %RANDOM
Rwork0.223 ---
obs0.226 29643 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.009 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å20 Å2-5.23 Å2
2---0.21 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 0 23 5575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225637
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9747616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30925.543267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.704151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0991529
X-RAY DIFFRACTIONr_chiral_restr0.0990.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024210
X-RAY DIFFRACTIONr_nbd_refined0.220.22476
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.26
X-RAY DIFFRACTIONr_mcbond_it0.5951.53628
X-RAY DIFFRACTIONr_mcangle_it1.02625672
X-RAY DIFFRACTIONr_scbond_it1.4832232
X-RAY DIFFRACTIONr_scangle_it2.3884.51944
LS refinement shellResolution: 2.59→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 79 -
Rwork0.292 1466 -
all-1545 -
obs--68.51 %
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)
15.3299-1.87020.9522.6693-0.12380.335-0.2967-0.41520.7109-0.53320.27241.0551-0.3259-0.74710.02430.05850.1167-0.16690.39770.26620.3688-31.0918-19.6075-32.9334
27.45591.47362.44465.17960.98010.852-0.38361.42080.8116-1.14120.20790.8459-0.0081-0.28890.17570.18150.0047-0.23230.29880.33370.2481-23.5256-24.8807-38.5938
34.08220.19630.47013.8071-1.04851.8984-0.1242-0.10590.5075-0.12530.23360.6096-0.1598-0.1732-0.10940.18290.02160.11530.2410.09380.2565-13.9337-27.6224-23.7172
43.3218-0.15120.7081.9594-0.67351.60660.07820.2255-0.0449-0.23060.01940.13240.04760.0146-0.09760.23430.01050.10120.3083-0.00040.12752.9564-35.7608-23.2002
56.33390.03342.31282.1321-1.02411.67480.0632-0.0817-0.14340.015-0.0928-0.1936-0.09620.17810.02950.19070.02350.14390.2682-0.02150.028611.4325-37.2926-15.4154
611.06315.95165.73843.27063.11032.9843-0.13060.47530.31-0.1640.06750.0867-0.05140.55770.0631-0.0364-0.0837-0.26020.44340.35760.4093-53.4919-40.8864-42.3948
74.32344.68890.33335.11640.27270.45220.3888-0.28810.41650.2404-0.13050.49950.123-0.0735-0.25840.101-0.05440.0610.1590.04430.2066-78.5719-30.9437-58.7758
83.44324.64210.59496.29020.67040.6484-0.04360.4429-0.3818-0.16740.3272-0.5392-0.04690.0136-0.28360.087-0.00290.05890.1270.04280.3065-69.3363-24.8057-61.9199
98.80291.34654.86190.9090.74614.18480.9195-0.0508-1.03730.1524-0.1459-0.30680.8527-0.017-0.77360.31080.0028-0.4008-0.01590.16250.4248-74.0523-57.4763-50.956
107.33897.38461.3068.49210.73670.74990.8908-0.3621-0.59330.9714-0.3563-0.77580.0641-0.018-0.53450.1734-0.08670.01830.13370.0520.2099-74.7984-31.8345-56.7256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 621 - 61
2X-RAY DIFFRACTION2AA63 - 11462 - 113
3X-RAY DIFFRACTION3AA115 - 162114 - 161
4X-RAY DIFFRACTION4AA163 - 290162 - 289
5X-RAY DIFFRACTION5AA291 - 348290 - 347
6X-RAY DIFFRACTION6AA349 - 392348 - 391
7X-RAY DIFFRACTION7AA393 - 471392 - 470
8X-RAY DIFFRACTION8AA472 - 533471 - 532
9X-RAY DIFFRACTION9AA534 - 646533 - 645
10X-RAY DIFFRACTION10AA647 - 698646 - 697

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