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- PDB-7xfr: Crystal structure of WIPI2b in complex with the second site of ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 7xfr
TitleCrystal structure of WIPI2b in complex with the second site of ATG16L1
Components
  • Autophagy-related protein 16-1
  • Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
KeywordsPROTEIN BINDING / WIPI2b / ATG16L1
Function / homology
Function and homology information


C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / dendrite arborization / xenophagy / corpus callosum development / protein localization to phagophore assembly site ...C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / dendrite arborization / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / negative stranded viral RNA replication / endolysosome membrane / axonal transport / Macroautophagy / autophagosome membrane / axoneme / autophagosome assembly / protein-membrane adaptor activity / sperm midpiece / positive regulation of autophagy / autophagosome / hippocampus development / macroautophagy / protein transport / GTPase binding / defense response to virus / axon / glutamatergic synapse / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / WD domain, G-beta repeat / 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. / WD40 repeats ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / WD domain, G-beta repeat / 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. / 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 / Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGong, X.Y. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Sci Adv / Year: 2023
Title: ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy.
Authors: Gong, X. / Wang, Y. / Tang, Y. / Wang, Y. / Zhang, M. / Li, M. / Zhang, Y. / Pan, L.
History
DepositionApr 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1
C: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)86,2534
Polymers86,2534
Non-polymers00
Water7,638424
1
A: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
B: Autophagy-related protein 16-1

C: Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)86,2534
Polymers86,2534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)74.199, 80.630, 76.755
Angle α, β, γ (deg.)90.000, 97.326, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2 / WIPI-2 / WIPI49-like protein 2


Mass: 35310.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WIPI2, CGI-50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4P8-2
#2: Protein Autophagy-related protein 16-1 / APG16-like 1


Mass: 7815.774 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate(pH 6.5), 12% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→73.59 Å / Num. obs: 83257 / % possible obs: 93.71 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.73 Å2 / Rrim(I) all: 0.037 / Net I/av σ(I): 24.4 / Net I/σ(I): 24.71
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 4440 / Rrim(I) all: 0.748

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTG

5ltg


Resolution: 1.76→24.99 Å / SU ML: 0.1383 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 4058 4.88 %
Rwork0.1645 79140 -
obs0.1659 83198 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.27 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 0 424 6356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086110
X-RAY DIFFRACTIONf_angle_d0.97228269
X-RAY DIFFRACTIONf_chiral_restr0.0584963
X-RAY DIFFRACTIONf_plane_restr0.00791070
X-RAY DIFFRACTIONf_dihedral_angle_d15.50692305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.25491620.22752879X-RAY DIFFRACTION99.97
1.78-1.80.25961510.21482884X-RAY DIFFRACTION99.97
1.8-1.830.20561370.19582942X-RAY DIFFRACTION100
1.83-1.850.2261560.1942870X-RAY DIFFRACTION100
1.85-1.880.23971680.18922891X-RAY DIFFRACTION100
1.88-1.90.24741710.18612850X-RAY DIFFRACTION100
1.9-1.930.199820.19161652X-RAY DIFFRACTION56.83
1.93-1.960.22121430.172926X-RAY DIFFRACTION100
1.96-1.990.21071480.1672914X-RAY DIFFRACTION100
1.99-2.030.20051670.16862861X-RAY DIFFRACTION99.97
2.03-2.060.21381320.17172689X-RAY DIFFRACTION96.21
2.09-2.10.2108560.1611350X-RAY DIFFRACTION99.58
2.1-2.150.21311510.16012886X-RAY DIFFRACTION100
2.15-2.190.20641610.16692910X-RAY DIFFRACTION100
2.19-2.240.18921340.16692659X-RAY DIFFRACTION98.62
2.26-2.30.2177850.16991766X-RAY DIFFRACTION98.98
2.3-2.360.17711620.17212912X-RAY DIFFRACTION99.97
2.36-2.430.21311440.16852929X-RAY DIFFRACTION99.93
2.43-2.510.21631350.16622914X-RAY DIFFRACTION100
2.51-2.60.18031450.17072900X-RAY DIFFRACTION100
2.6-2.70.21871480.17972902X-RAY DIFFRACTION100
2.7-2.830.21681500.17562925X-RAY DIFFRACTION99.94
2.83-2.980.21591360.1722946X-RAY DIFFRACTION99.87
2.98-3.160.19191610.17582893X-RAY DIFFRACTION99.97
3.16-3.410.20931440.17232911X-RAY DIFFRACTION99.9
3.41-3.750.18491040.15612299X-RAY DIFFRACTION78.04
3.75-4.290.17551300.1482767X-RAY DIFFRACTION93.27
4.29-5.390.13391490.12832947X-RAY DIFFRACTION99.87
5.39-24.990.20011460.17982966X-RAY DIFFRACTION98.61

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