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- PDB-2oew: Structure of ALIX/AIP1 Bro1 Domain -

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Basic information

Entry
Database: PDB / ID: 2oew
TitleStructure of ALIX/AIP1 Bro1 Domain
ComponentsProgrammed cell death 6-interacting protein
KeywordsPROTEIN TRANSPORT / Tetratricopeptide repeat / TPR
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 / protein homooligomerization / Budding and maturation of HIV virion / 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
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFisher, R.D. / Zhai, Q. / Robinson, H. / Hill, C.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural and Biochemical Studies of ALIX/AIP1 and Its Role in Retrovirus Budding
Authors: Fisher, R.D. / Chung, H.Y. / Zhai, Q. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
History
DepositionJan 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)42,7361
Polymers42,7361
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.678, 63.243, 76.384
Angle α, β, γ (deg.)90.00, 122.15, 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: 42735.789 Da / Num. of mol.: 1 / Fragment: Bro1 Domain, residues 1-359
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) / Strain (production host): BL21 (DE3) Codon + (RIL) / References: UniProt: Q8WUM4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 20000, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 16063 / Num. obs: 15487 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.6
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.6 / % possible all: 79.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å29.99 Å
Translation2.6 Å29.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.3.0008refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZB1

1zb1


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.14 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27386 783 5.1 %RANDOM
Rwork0.20827 ---
obs0.21167 14704 96.43 %-
all-16079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.059 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å21.05 Å2
2--3.3 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 0 82 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9693896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84425.267131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1131511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022155
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21361
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21961
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7551.51846
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25322887
X-RAY DIFFRACTIONr_scbond_it1.7831159
X-RAY DIFFRACTIONr_scangle_it2.824.51006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.549→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 48 -
Rwork0.289 859 -
obs--77.46 %
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)
119.67376.7744-4.37232.5736-1.74873.6439-0.49580.0794-0.81580.01070.0269-0.09860.5955-0.27160.46890.265-0.10180.02560.1851-0.06710.24114.600120.346224.5862
227.18244.048-2.76820.6132-0.5171.34311.07470.31940.83220.5251-0.73711.8113-2.2744-1.2451-0.33760.5369-0.0038-0.00040.53620.00150.5372-15.916528.423322.1912
315.92992.9643-2.93875.0716-2.75574.4404-0.61350.9044-0.4868-0.55730.36-0.00940.9035-0.37710.25350.1315-0.1489-0.00970.243-0.16070.12675.173722.031517.7907
47.55558.359-1.577419.4043-12.111110.90930.3888-1.02881.96883.4554-0.07631.3447-1.5783-1.5994-0.31250.4853-0.0013-0.00610.48510.00140.4884-5.524335.720128.6481
54.34292.0082-6.15627.6627-1.41399.03160.3718-1.8647-0.94810.7099-0.6731-0.19410.49260.26830.30130.2126-0.22080.0060.44120.03130.175811.061821.030536.1779
66.82412.6474-6.46881.027-2.50966.1320.6165-1.0914-1.0838-0.4036-1.10420.40061.40070.49230.48760.4008-0.05220.03230.4005-0.03080.3957.130624.694637.3303
76.45980.0459-3.15522.43460.1063.7577-0.32170.8026-0.104-0.30650.01460.03790.2423-0.41920.30710.1897-0.1091-0.05760.2662-0.08540.161718.421725.301115.1381
84.75530.1426-1.0523.6331-0.76014.81060.06580.17590.65540.10530.01890.1237-0.5236-0.2586-0.08470.1154-0.0395-0.04070.1818-0.06520.237117.97334.426921.4649
95.53391.2466-1.96071.7111-0.38473.9475-0.02250.09190.28890.0225-0.03830.2108-0.0865-0.10860.06080.2394-0.0226-0.04980.1991-0.01380.231627.786533.490320.2404
102.696-0.4689-2.73130.60361.95686.973-0.114-0.5279-0.24880.2699-0.2451-0.00950.3917-0.37650.35910.1732-0.0446-0.00460.21890.04220.164131.600726.06731.3345
112.88510.5029-1.72141.7892-1.06281.5696-0.03890.0298-0.0001-0.0535-0.00920.00820.08480.03280.04810.1872-0.0236-0.02350.2339-0.01940.118249.187232.22213.8129
126.27330.558-2.13410.7677-0.39471.39790.01430.41590.1126-0.0728-0.01520.13390.098-0.11810.00080.1825-0.0508-0.05770.1417-0.04470.067837.602431.77213.4729
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 1722 - 38
2218 - 4539 - 66
3346 - 7467 - 95
4475 - 8996 - 110
5590 - 105111 - 126
66106 - 116127 - 137
77117 - 152138 - 173
88153 - 165174 - 186
99166 - 230187 - 251
1010231 - 247252 - 268
1111248 - 290269 - 311
1212291 - 358312 - 379

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