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- PDB-2ojq: Crystal structure of Alix V domain -

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Basic information

Entry
Database: PDB / ID: 2ojq
TitleCrystal structure of Alix V domain
ComponentsProgrammed cell death 6-interacting protein
KeywordsAPOPTOSIS / helical
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 / Budding and maturation of HIV virion / protein homooligomerization / 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 in complex with the ypdl late domain / 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 ...alix/aip1 in complex with the ypdl late domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death 6-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.87 Å
AuthorsLee, S. / Hurley, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for viral late-domain binding to Alix
Authors: Lee, S. / Joshi, A. / Nagashima, K. / Freed, E.O. / Hurley, J.H.
History
DepositionJan 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE Ser 555 agrees with the Gene Bank entry AF349951

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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)39,1931
Polymers39,1931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.650, 55.380, 113.166
Angle α, β, γ (deg.)90.00, 92.37, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / Hp95


Mass: 39193.406 Da / Num. of mol.: 1 / Fragment: V domain, residues 360-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Plasmid: pGST2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WUM4

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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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 13-15% PEG 6000, 6-10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795, 0.9799, 0.9600
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006 / Details: mirror
RadiationMonochromator: Si(111), Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97991
30.961
ReflectionResolution: 2.9→113 Å / Num. obs: 10483 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 78.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.1 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.87→113.23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.875 / SU B: 45.038 / SU ML: 0.403 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31844 1030 9.9 %RANDOM
Rwork0.24986 ---
obs0.2566 9414 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.861 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å23.66 Å2
2---3.24 Å20 Å2
3---6.58 Å2
Refinement stepCycle: LAST / Resolution: 2.87→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 0 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9813688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.64625.821134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.3081519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.21404
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21876
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4971.51761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84322767
X-RAY DIFFRACTIONr_scbond_it1.46131070
X-RAY DIFFRACTIONr_scangle_it2.3214.5921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.871→2.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 61 -
Rwork0.303 542 -
obs--76.33 %
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)
17.8579-0.5155-5.52451.16010.86315.7807-0.9162-1.3701-1.38090.77690.15460.3741.25360.30770.76170.07590.0330.18310.04920.34540.31624.252423.930428.7648
22.86550.1918-0.67157.6006-6.84559.5998-0.0663-1.1019-0.04861.57660.47510.7648-0.8219-0.6885-0.4088-0.15340.09690.072-0.0419-0.0425-0.3843-5.105649.621524.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA360 - 4106 - 56
2X-RAY DIFFRACTION1AA540 - 642186 - 288
3X-RAY DIFFRACTION2AA411 - 53957 - 185
4X-RAY DIFFRACTION2AA643 - 702289 - 348

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