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- PDB-6klr: Crystal structure of human WIPI3 in complex with the WIR-peptide ... -

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Basic information

Entry
Database: PDB / ID: 6klr
TitleCrystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A
Componentschimera ATG2A and WIPI3
KeywordsLIPID BINDING PROTEIN / MEMBRANE BOUND PROTEIN
Function / homology
Function and homology information


TSC1-TSC2 complex binding / organelle membrane contact site / phagophore / protein lipidation / lipid transfer activity / glycophagy / nucleophagy / positive regulation of autophagosome assembly / autophagy of mitochondrion / protein localization to phagophore assembly site ...TSC1-TSC2 complex binding / organelle membrane contact site / phagophore / protein lipidation / lipid transfer activity / glycophagy / nucleophagy / positive regulation of autophagosome assembly / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / phagophore assembly site / reticulophagy / phosphatidylinositol-3,5-bisphosphate binding / Macroautophagy / extrinsic component of membrane / autophagosome assembly / protein-membrane adaptor activity / cellular response to starvation / lipid droplet / lysosome / endoplasmic reticulum membrane / cytosol
Similarity search - Function
Autophagy-related protein 2/VPS13, C-terminal / Autophagy-related protein 2 / ATG2/VPS13, C terminal domain / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / VPS13-like, N-terminal / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 2 homolog A / WD repeat domain phosphoinositide-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRen, J.Q. / Liang, R.B. / Feng, W.
CitationJournal: Nat Commun / Year: 2020
Title: Multi-site-mediated entwining of the linear WIR-motif around WIPI beta-propellers for autophagy.
Authors: Ren, J. / Liang, R. / Wang, W. / Zhang, D. / Yu, L. / Feng, W.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimera ATG2A and WIPI3
B: chimera ATG2A and WIPI3


Theoretical massNumber of molelcules
Total (without water)76,9202
Polymers76,9202
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, A chain and B chain forms a complex with the molar ratio of 1:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.124, 121.063, 37.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein chimera ATG2A and WIPI3 / WIPI-3 / WD repeat-containing protein 45-like / WDR45-like protein / WD repeat-containing protein ...WIPI-3 / WD repeat-containing protein 45-like / WDR45-like protein / WD repeat-containing protein 45B / WIPI49-like protein


Mass: 38459.828 Da / Num. of mol.: 2 / Mutation: Deletion of 75-80 and Deletion of 264-280
Source method: isolated from a genetically manipulated source
Details: The sequence provided here is chimeric. We fused ATG2A (1374-1404) to the N-terminal of WIPI3. And we also deleted two loops in WIPI3 (Loop1: 75-80; loop2: 264-281). The first four residues ...Details: The sequence provided here is chimeric. We fused ATG2A (1374-1404) to the N-terminal of WIPI3. And we also deleted two loops in WIPI3 (Loop1: 75-80; loop2: 264-281). The first four residues (GPGS) is the expression tag. Residues form 5 to 35 (PRDGEPVVTQLHPGPIVVRDGYFSRPIGSTD) is the fused ATG2A sequence (from 1374 to 1404). Residues from 36 to 37 (GS) is the linker. The rest part is form WIPI3.
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG2A, KIAA0404, WDR45B, WDR45L, WIPI3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TAZ0, UniProt: Q5MNZ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.44 Å3/Da / Density % sol: 48.01 %
Description: Authors state that Sfcheck gives the Matthews coefficient about 2.44, Phenix.Xtriage gives 2.18.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tirs-HCl, pH 8.5, 20% (v/v) Ethanol / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17842 / % possible obs: 99.3 % / Redundancy: 11.6 % / Biso Wilson estimate: 53.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Χ2: 0.934 / Net I/av σ(I): 20.6 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1650 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.149 / Rrim(I) all: 0.451 / Χ2: 0.745 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IYY

6iyy


Resolution: 2.21→24.52 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.27
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 864 4.9 %Random selection
Rwork0.2126 ---
obs0.2147 17638 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.12 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.21→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 0 18 2469
Biso mean---67.47 -
Num. residues----319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.350.42891520.35982606275895
2.35-2.530.34591520.29452737288999
2.53-2.780.30231320.24962788292099
2.78-3.190.3021350.244728262961100
3.19-4.010.26011340.216828592993100
4.01-24.520.21521590.1782958311798
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)
15.91920.701-1.33233.73470.26051.643-0.22690.17180.8958-0.18970.26150.46650.1877-0.0879-0.0030.5061-0.0364-0.10490.49570.01760.486990.9591137.017846.244
21.3229-1.3322-0.52222.10930.16251.288-0.1205-0.3120.9828-0.1393-0.1951-1.11520.11750.3004-0.3450.62020.00890.07060.9183-0.20091.1166111.1411141.997346.1801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 9 through 311)A9 - 311
2X-RAY DIFFRACTION2(chain 'B' and resid 1378 through 1399)B1378 - 1399

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