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- PDB-6iyy: Crystal structure of human WIPI3,loop deletion mutant -

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Basic information

Entry
Database: PDB / ID: 6iyy
TitleCrystal structure of human WIPI3,loop deletion mutant
ComponentsWD repeat domain phosphoinositide-interacting protein 3
KeywordsLIPID BINDING PROTEIN / MEMBRANE BOUND PROTEIN
Function / homology
Function and homology information


TSC1-TSC2 complex binding / protein lipidation / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phagophore assembly site / phosphatidylinositol-3,5-bisphosphate binding / Macroautophagy ...TSC1-TSC2 complex binding / protein lipidation / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phagophore assembly site / phosphatidylinositol-3,5-bisphosphate binding / Macroautophagy / extrinsic component of membrane / autophagosome assembly / cellular response to starvation / lysosome / cytosol
Similarity search - Function
WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat domain phosphoinositide-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.796 Å
AuthorsLiang, R.B. / Ren, J.Q. / Feng, W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470746 China
National Natural Science Foundation of China31770786 China
National Natural Science Foundation of China31600608 China
National Natural Science Foundation of China31600622 China
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Conservation of the Two Phosphoinositide-Binding Sites in WIPI Proteins.
Authors: Liang, R. / Ren, J. / Zhang, Y. / Feng, W.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat domain phosphoinositide-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6398
Polymers34,9671
Non-polymers6727
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.297, 104.931, 124.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

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Components

#1: Protein WD repeat domain phosphoinositide-interacting protein 3 / WIPI-3


Mass: 34966.996 Da / Num. of mol.: 1 / Mutation: DELETION OF RESIDUES 75-80 and 264-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WIPI3 / Plasmid: pET32a / Details (production host): N-terminal GB1 tag / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5MNZ6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7 / Details: 1.6M Ammonium Sulfate, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 28765 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3 / Num. unique obs: 1811 / CC1/2: 0.99 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.12_2829: ???refinement
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.796→42.357 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.69
RfactorNum. reflection% reflection
Rfree0.2041 1999 6.95 %
Rwork0.1654 --
obs0.1681 28761 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.53 Å2 / Biso mean: 23.6258 Å2 / Biso min: 8.89 Å2
Refinement stepCycle: final / Resolution: 1.796→42.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 35 187 2618
Biso mean--42.63 30.93 -
Num. residues----312
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)
13.1244-1.4847-0.54444.1334-1.30883.0337-0.0725-0.1647-0.11110.1090.0025-0.03780.00550.00740.05210.0966-0.0078-0.00370.0895-0.00040.1120.22819.897-7.5084
21.80821.7994-1.10982.9028-0.70271.62280.0261-0.0748-0.33090.01730.0172-0.34390.08120.1071-0.06120.1170.0196-00.1215-0.02090.186311.33866.7847-14.5393
33.40660.3765-0.06884.2571.82385.7533-0.05480.2227-0.3555-0.29110.2419-0.52970.05980.2805-0.17020.10020.00770.05310.1355-0.03060.172119.398614.4231-22.4798
42.05470.38250.88232.6490.9743.64520.01170.18410.1068-0.29780.0849-0.1645-0.1730.0562-0.0950.1271-0.00490.02920.11430.00910.104111.658827.8964-20.7737
52.62240.8527-0.88011.6929-0.51441.82190.06240.15930.2252-0.04750.02530.1233-0.1048-0.0953-0.05810.10520.0335-0.00660.11920.00320.1108-5.266428.3084-9.7351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 44 )A1 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 99 )A45 - 99
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 127 )A100 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 195 )A128 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 312 )A196 - 312

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