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- PDB-7mu2: Crystal Structure of WIPI2 in complex with W2IR of ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 7mu2
TitleCrystal Structure of WIPI2 in complex with W2IR of ATG16L1
Components
  • Autophagy-related protein 16-1
  • WD repeat domain phosphoinositide-interacting protein 2
KeywordsLIPID BINDING PROTEIN / Autophagy / WIPI2 / ATG16
Function / homology
Function and homology information


protein lipidation involved in autophagosome assembly / xenophagy / protein localization to phagophore assembly site / negative stranded viral RNA replication / axoneme / autophagosome membrane / positive regulation of autophagy
Similarity search - Function
Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / : / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / : / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 16-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStrong, L.M. / Flower, T.G. / Buffalo, C.Z. / Hurley, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
Michael J. Fox FoundationASAP-000350 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM111730 United States
CitationJournal: Elife / Year: 2021
Title: Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy.
Authors: Strong, L.M. / Chang, C. / Riley, J.F. / Boecker, C.A. / Flower, T.G. / Buffalo, C.Z. / Ren, X. / Stavoe, A.K. / Holzbaur, E.L. / Hurley, J.H.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1
C: WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)77,2094
Polymers77,2094
Non-polymers00
Water11,259625
1
A: WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)38,6042
Polymers38,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-4 kcal/mol
Surface area14390 Å2
MethodPISA
2
C: WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)38,6042
Polymers38,6042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.771, 49.075, 120.130
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein WD repeat domain phosphoinositide-interacting protein 2 / WIPI2


Mass: 35606.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Protein/peptide Autophagy-related protein 16-1


Mass: 2997.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: E7EVC7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 22% w/v PEG 3,350, 2% v/v Tacsimate pH 7.0, 100mM Hepes pH 7.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→38.94 Å / Num. obs: 55829 / % possible obs: 98.5 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.068 / Net I/σ(I): 6.9
Reflection shellResolution: 1.85→1.97 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5022 / Rrim(I) all: 0.031

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EXV

4exv


Resolution: 1.85→38.94 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 885 1.6 %
Rwork0.1831 --
obs0.1837 55472 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5041 0 0 625 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075123
X-RAY DIFFRACTIONf_angle_d0.9066917
X-RAY DIFFRACTIONf_dihedral_angle_d18.1941882
X-RAY DIFFRACTIONf_chiral_restr0.063801
X-RAY DIFFRACTIONf_plane_restr0.005891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.970.30391410.24368375X-RAY DIFFRACTION88
1.97-2.120.2471420.20618702X-RAY DIFFRACTION91
2.12-2.330.25771380.19699002X-RAY DIFFRACTION94
2.33-2.670.24521490.19469361X-RAY DIFFRACTION98
2.67-3.360.21691550.17889458X-RAY DIFFRACTION98
3.36-38.940.17151600.16049689X-RAY DIFFRACTION98

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