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- PDB-8zqg: Crystal structure of WIPI3 in complex with ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 8zqg
TitleCrystal structure of WIPI3 in complex with ATG16L1
Components
  • Autophagy-related protein 16-1
  • WD repeat domain phosphoinositide-interacting protein 3
KeywordsPROTEIN BINDING / WIPI3 / ATG16L1
Function / homology
Function and homology information


C-terminal protein lipidation / TSC1-TSC2 complex binding / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / glycophagy / nucleophagy / dendrite arborization ...C-terminal protein lipidation / TSC1-TSC2 complex binding / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / glycophagy / nucleophagy / dendrite arborization / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / pexophagy / phosphatidylinositol-3-phosphate binding / negative stranded viral RNA replication / endolysosome membrane / phagophore assembly site / phosphatidylinositol-3,5-bisphosphate binding / axonal transport / Macroautophagy / autophagosome membrane / axoneme / autophagosome assembly / protein-membrane adaptor activity / sperm midpiece / positive regulation of autophagy / autophagosome / cellular response to starvation / hippocampus development / macroautophagy / protein transport / GTPase binding / protein-macromolecule adaptor activity / defense response to virus / lysosome / axon / glutamatergic synapse / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / : / PROPPIN / 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. ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / : / PROPPIN / 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
WD repeat domain phosphoinositide-interacting protein 3 / Autophagy-related protein 16-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsGong, X.Y. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Cells / Year: 2024
Title: Structure of the WIPI3/ATG16L1 Complex Reveals the Molecular Basis for the Recruitment of the ATG12~ATG5-ATG16L1 Complex by WIPI3.
Authors: Gong, X. / Wang, Y. / Zhou, Y. / Pan, L.
History
DepositionJun 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: WD repeat domain phosphoinositide-interacting protein 3
C: Autophagy-related protein 16-1
D: Autophagy-related protein 16-1
A: WD repeat domain phosphoinositide-interacting protein 3


Theoretical massNumber of molelcules
Total (without water)86,9614
Polymers86,9614
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.663, 182.663, 54.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein WD repeat domain phosphoinositide-interacting protein 3 / 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: 35664.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR45B, WDR45L, WIPI3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MNZ6
#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.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8); 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.77→91.33 Å / Num. obs: 26763 / % possible obs: 100 % / Redundancy: 17.2 % / Biso Wilson estimate: 76.23 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 16.1
Reflection shellResolution: 2.77→2.82 Å / Num. unique obs: 1330 / Rpim(I) all: 0.435

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IYY

6iyy


Resolution: 2.77→43.87 Å / SU ML: 0.3576 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1369 5.12 %
Rwork0.1899 25359 -
obs0.192 26728 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.6 Å2
Refinement stepCycle: LAST / Resolution: 2.77→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5617 0 0 14 5631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085735
X-RAY DIFFRACTIONf_angle_d1.21627772
X-RAY DIFFRACTIONf_chiral_restr0.0722878
X-RAY DIFFRACTIONf_plane_restr0.00931013
X-RAY DIFFRACTIONf_dihedral_angle_d15.63252084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.870.33891420.27952514X-RAY DIFFRACTION100
2.87-2.980.30731310.23582518X-RAY DIFFRACTION99.96
2.98-3.120.28861290.26622514X-RAY DIFFRACTION100
3.12-3.280.27371410.21732494X-RAY DIFFRACTION100
3.29-3.490.25761440.21122527X-RAY DIFFRACTION100
3.49-3.760.23911730.1962476X-RAY DIFFRACTION100
3.76-4.140.22881380.19632558X-RAY DIFFRACTION99.96
4.14-4.740.18471290.15622539X-RAY DIFFRACTION99.93
4.74-5.960.21651220.18452582X-RAY DIFFRACTION100
5.97-43.870.21821200.16872637X-RAY DIFFRACTION99.1
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)
14.79322589164-0.61976478947-0.3908898521712.48124231373-2.86447442073.90670811980.2858443765730.183387964549-0.454518801524-0.452969880502-0.05712468367620.8352280223830.317859226621-0.264277193269-0.186489083790.708823241033-0.046534858918-0.09337362572650.636252529553-0.104263808730.941066750558-62.4278300115-52.8071181544-36.9014097217
24.233139512271.954638654172.772070666195.33642935518-2.645298139666.027755800870.1716544806180.379448617785-0.188265327747-0.417366906383-0.3264353590010.4755893348580.218720219334-0.6650839907270.1370906035090.5696846735290.0501544434942-0.08421010617680.63647834764-0.02150210965450.712691312061-55.3367186441-47.8446021265-40.4632267794
32.929645615741.305824348490.8236772620532.702389773841.224135181955.23285895334-0.04227950113330.2727319873340.0114723834619-0.306340475704-0.0374034104913-0.08185767277730.1450128512620.2050265201290.07755338758980.4817180368470.0900859815037-0.01818360033090.5079940748980.04298656514820.442758687177-46.0557134292-42.9176714462-38.7512598952
42.94335627865-0.350859881496-2.206607524336.46253803754-0.810515399616.3373675364-0.0381295816531-0.4128320446130.1914684108490.5324816821590.03982096865670.202690699492-0.1747633210270.3224468177810.05008995169550.4544045830890.0354458404255-0.02125376222060.460781198068-0.04292281068520.458981940806-47.6933465489-41.6749674124-19.5588508698
55.819233801152.749286807660.7546805506114.47287015206-0.8169534570915.65158213140.147023616979-0.526290987863-0.3065738186630.76703505596-0.08093223419870.3849865551310.657615991341-0.07983002598830.0093037616190.720011628640.05079458334470.1731191941180.596191778817-0.01116912411420.661893951549-57.137934336-51.1333084441-12.7396561714
64.35222751174-0.907415368292-2.28749692527.965443526355.735810714532.07096520823-0.808303657613-0.73773761399-1.001880828860.1788331660190.1980979295841.227579070610.5437454094290.1429971531120.5758489390851.02659102821-0.09087762058690.1486596952520.8274677457330.2536744100720.939902955333-64.2109800622-55.8728795996-11.5913052505
74.517502068810.861281004419-0.7002013914944.994817033290.06241061515838.32739349241-0.1841530796960.153741870893-0.458101719283-0.1524544502290.311112805495-0.3605186367651.05768477332-0.852382970646-0.2009894737460.736861935084-0.133923760615-0.04584972874050.600492977917-0.06908221259980.961896807195-70.0655994187-57.6269706868-24.2485956348
86.773857631983.56379337732-0.2339715602926.75531809687-0.1302582962972.510428952750.3100458663070.02302003222660.494386065060.417169491195-0.334367664702-0.541156061983-0.4240069614210.883346528318-0.05125371291490.731495457843-0.0381370688516-0.079374515380.6703806054420.05436404963210.542142883127-47.9230800488-24.6835471952-44.0366602119
96.444387023642.280992517591.330619015463.324736697661.221564837963.29705828646-0.1846542034510.1715572380420.4551477107670.05959914408240.166236920823-0.320758674922-0.5735938406140.6596398378420.04602754558350.843439351308-0.010168716946-0.1223635206290.6408283993270.1182931117790.558023634819-50.516562055-19.1167732499-43.4022047169
107.122214828952.65201148537-0.1545952452768.777776209621.687041561539.836267862950.213507440406-0.152543602663-0.105382586840.214016167236-0.0007356100966580.5687271683-0.0721624111387-1.29211418166-0.2750454145650.4634785750160.0258368108451-0.04601632027450.6545092890670.05149887352260.587393413326-78.2820565978-15.2398073137-58.3724025133
117.237509113840.683338615705-0.03577478965742.382140422590.5617676165477.677987640720.170005812789-0.267544718254-0.1771160803320.7053218627280.1376219563460.240988700879-0.104488705636-0.61805006937-0.2676524580380.5820358108590.00494073872398-0.01163258566820.4125911727520.01303547644870.359556692225-66.2067688687-9.91594980493-52.3821350487
122.838902944430.2532030173230.8266041741572.703538440240.8421807170616.96978017898-0.02064317870980.656067645747-0.189178047121-0.1984723973190.100904895745-0.0553361534089-0.4475100190670.567239438411-0.07401309522840.426383623354-0.00778601653781-0.000260315397460.521026855723-0.04164647177550.436905790345-59.8295237876-12.0464103801-72.1189991478
138.59528189896-1.0592347258-6.891717733174.42693923943.497789932039.55029985827-0.276881314071.24522127647-0.970726264486-0.524888047675-0.05989202390810.4844903283920.0320422121054-0.752583147140.656985280560.838708748656-0.0998028011625-0.1555397490260.903551386128-0.1057758580130.529941357099-72.6497989637-18.0503144052-83.9720777693
145.09787425924-0.685840119633-3.247921395088.190714566712.059392184566.14928727112-0.1403621918881.26571138405-0.673247495357-0.489152132788-0.3559929388250.8105646672310.22131939684-1.660741574830.4416041281040.535130125493-0.0438273589332-0.04485168186151.04314494273-0.1572303160410.811562593062-81.3400280244-21.6865099188-74.1608246153
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 12 through 48 )BA12 - 481 - 37
22chain 'B' and (resid 49 through 71 )BA49 - 7138 - 60
33chain 'B' and (resid 72 through 136 )BA72 - 13661 - 125
44chain 'B' and (resid 137 through 204 )BA137 - 204126 - 193
55chain 'B' and (resid 205 through 258 )BA205 - 258194 - 247
66chain 'B' and (resid 259 through 296 )BA259 - 296248 - 267
77chain 'B' and (resid 297 through 339 )BA297 - 339268 - 310
88chain 'C' and (resid 126 through 176 )CB126 - 1761 - 51
99chain 'D' and (resid 126 through 177 )DC126 - 1771 - 52
1010chain 'A' and (resid 10 through 59 )AD10 - 591 - 50
1111chain 'A' and (resid 60 through 124 )AD60 - 12451 - 115
1212chain 'A' and (resid 125 through 258 )AD125 - 258116 - 249
1313chain 'A' and (resid 259 through 296 )AD259 - 296250 - 269
1414chain 'A' and (resid 297 through 339 )AD297 - 339270 - 312

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