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- PDB-9jf2: Crystal structure of GABARAPL1 in complex with ATG16L1 -

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Basic information

Entry
Database: PDB / ID: 9jf2
TitleCrystal structure of GABARAPL1 in complex with ATG16L1
Components
  • Autophagy-related protein 16-1
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsPROTEIN BINDING / GABARAPL1 / 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 / glycophagy / dendrite arborization / xenophagy / corpus callosum development ...C-terminal protein lipidation / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / microautophagy / glycophagy / dendrite arborization / xenophagy / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / negative stranded viral RNA replication / endolysosome membrane / cellular response to nitrogen starvation / axonal transport / Macroautophagy / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / beta-tubulin binding / mitophagy / protein-membrane adaptor activity / sperm midpiece / positive regulation of autophagy / autophagosome / cytoplasmic vesicle membrane / hippocampus development / macroautophagy / phospholipid binding / protein transport / GTPase binding / defense response to virus / microtubule / cilium / ciliary basal body / axon / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / WD domain, G-beta repeat / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / WD domain, G-beta repeat / Ubiquitin-like domain superfamily / 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 / Gamma-aminobutyric acid receptor-associated protein-like 1
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: Nat Commun / Year: 2025
Title: Molecular bases of the interactions of ATG16L1 with FIP200 and ATG8 family proteins.
Authors: Gong, X. / Zhou, Y. / Wang, Y. / Tang, Y. / Liu, H. / Zhou, X. / Zhang, Y. / Guo, H. / Guo, Z. / Pan, L.
History
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Autophagy-related protein 16-1
D: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0086
Polymers31,7724
Non-polymers2362
Water3,387188
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
D: Autophagy-related protein 16-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1224
Polymers15,8862
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area7680 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)15,8862
Polymers15,8862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.147, 65.426, 109.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14366.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide Autophagy-related protein 16-1 / APG16-like 1


Mass: 1519.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q676U5
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000

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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: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→19.07 Å / Num. obs: 28146 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 13.57 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 11.3
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 1375 / Rpim(I) all: 0.116

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→19.07 Å / SU ML: 0.1778 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 1473 5.28 %
Rwork0.1895 26419 -
obs0.1908 27892 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.02 Å2
Refinement stepCycle: LAST / Resolution: 1.76→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 16 188 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992276
X-RAY DIFFRACTIONf_angle_d0.98173086
X-RAY DIFFRACTIONf_chiral_restr0.0561318
X-RAY DIFFRACTIONf_plane_restr0.0107407
X-RAY DIFFRACTIONf_dihedral_angle_d17.051874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.29581430.26692374X-RAY DIFFRACTION99.96
1.81-1.880.29631470.24482353X-RAY DIFFRACTION99.92
1.88-1.950.27011300.21682369X-RAY DIFFRACTION99.92
1.95-2.040.24571350.20852397X-RAY DIFFRACTION99.92
2.04-2.150.21081190.19322406X-RAY DIFFRACTION99.96
2.15-2.290.21211300.18042404X-RAY DIFFRACTION99.8
2.29-2.460.21120.17272413X-RAY DIFFRACTION100
2.46-2.710.18231630.17182408X-RAY DIFFRACTION99.81
2.71-3.10.17921280.18032429X-RAY DIFFRACTION99.61
3.1-3.90.17861380.16712460X-RAY DIFFRACTION99.54
3.9-19.070.21781280.18162406X-RAY DIFFRACTION92.58
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)
18.630507828252.43195621854-1.322127704153.87775432065-1.218790571290.426332705771-0.1100457804460.184569324731-0.524310004407-0.6979991311240.1238426126180.8631247450270.0472479148993-1.00424388664-0.01878477324960.334785807642-0.0734440796468-0.1223639132790.41858740154-0.05834294247270.3412692558935.22290147154-25.7341516417-5.75809499031
25.435430951282.74935255068-1.669545712659.62238920790.9013895701816.221070548570.207333614426-0.260448461973-0.87486799468-0.136316856685-0.115998564288-0.4063272286950.229850567572-0.258258963277-0.09942009100950.110300033772-0.0842712367735-0.04539044542110.2153487014010.005296139126410.16946761863214.5599647581-22.58091525890.429518255093
33.939568892770.6454396520.9263840209365.2601151121-2.777482995733.915741186620.156293784503-0.1320860062640.4626184635160.03906525676-0.09755722850890.0788128136259-1.101927205120.207163667584-0.04622315807210.366313737498-0.1113983386840.03663172184950.154981633199-0.06357043329640.13369792310611.1266309457-10.17840987161.30680861604
47.48482860738-0.9429237519010.9530255082845.760917981440.8358899344526.434739009740.09004539836010.08279396831410.504305720789-0.0977071288898-0.0360248960411-0.258596149126-0.735023749610.0781118952327-0.05088428515330.147864415141-0.09698353092520.0202872288470.121990911730.003889151777990.074487834988312.1001385795-11.4243814531-9.9071561637
54.403951321630.04937790048431.195596685454.32739334982-0.3427513054624.347169189650.05818796158010.0402067770197-0.170309448198-0.0626362725949-0.0741022450929-0.6061237194570.1264712888640.5092708989760.01227711966420.0819411943376-0.08472461646690.04637854919020.237671963174-0.009288129073090.11150351686115.4839483969-18.7085155073-13.8965228876
66.31132950359-3.61340041186-2.920002182444.362597682241.907346375735.915517721390.01771902202860.112941867740.5474266620470.07395868568320.0811210060967-0.531663793469-0.3637508666030.572564414301-0.07575924508540.101742037113-0.116752448113-0.02320665440140.215274909446-0.01782044978580.12008255646814.3838161474-16.49557412-22.1736084543
72.6020155592-0.0111398919893-0.5925735689221.97325523991.117958977486.163625534070.04980159184290.129796430546-0.251891734801-0.01828426297860.01777788443640.07980602514280.334368784252-0.201507716484-0.04541429506240.0916595106693-0.0778906332458-0.02585226424520.131263118317-0.0008388442159150.08198573483347.61228564588-20.9427410998-15.3925308553
89.789499357390.236186160702-1.667770975747.332166941641.020993081066.375448567870.277841744970.1780803983160.2819519652450.471784259448-0.3942995805831.38058227209-0.444234985077-1.23454004040.1195677850510.316859466695-0.001481586899650.1122693052740.316258443737-0.02951869568880.316116752856-13.8698094703-6.873706628925.26067679892
96.753307135890.601088339597-1.027707232467.759677710533.931063154399.336641949760.208385273130.3843307780880.28607872182-0.1069903816460.0544361814096-0.028986097963-0.707557059357-0.0728051316411-0.2646467913730.145255066938-0.06332643506420.003027223210910.1862030733280.02438153354270.0901527374415-4.31762861408-9.58919039034-0.713729484087
104.735944172541.15103393765-0.8900069621356.26786563892-4.401714041315.566162663370.1390128344450.1930445238-0.7857800599240.00219901760912-0.0362457309885-0.1485603511681.26067550057-0.0967391814809-0.09536862265980.46608958332-0.0350571686074-0.09754716932840.193852989278-0.07508764897860.203683710741-7.90077302757-22.1767852727-1.92568031782
117.263990178440.552412997198-0.7469903908942.00020368475-0.1191767225726.784704716650.0708091069747-0.00968934381239-0.8033519020040.120100468769-0.06014730673980.02080046009080.743126889976-0.12692373022-0.00115824555220.190730191445-0.140115550316-0.009146730957070.1143726571830.03859932334820.166832057765-6.91929101896-21.17765510669.2818610555
123.506654270340.331876646658-0.5073309883794.137503597152.093892663223.596348155390.150790591458-0.01346552531060.61102950566-0.04762919948430.127171588316-0.607331230438-0.6982909157390.41216243545-0.2673088154130.308986078167-0.1515777669020.01958349209130.2325103127710.03256412677140.245828509-0.628845392405-6.7401526716412.7282380314
133.468207419110.643114172326-0.8090696336222.831105149783.053931736376.053009457610.129981871613-0.229009088177-0.4240422274960.2372337930280.0320386376585-0.2729475570850.3794664710180.231302953076-0.1292427739640.133083305623-0.0715412148783-0.03326356711660.1415238290520.06691029170550.133217066027-5.35400309259-19.070533276318.4599995632
141.753844456290.3932730363670.2895333810081.105715634910.5433276656274.350823021630.108531640727-0.0862529129456-0.02090136556840.03794065571460.09290250152290.06386322693410.0152454036752-0.257898951204-0.1230725827220.0480020698083-0.189917599862-0.03573123910770.1822830847740.03375880908140.103897891732-11.524329448-13.504107559314.4490260386
155.32786184717-0.9067075268460.9227667229991.65859772018-2.432793097813.60271867505-0.0822093847895-0.07980805294030.796610284874-0.1244290542490.122178894239-0.0622343614443-1.398697420330.16263468857-0.03668260488170.455483010636-0.09008714120280.01771421659360.2411230435670.0104539084070.252480264445-10.8994187428-0.10570100042616.9434886902
169.58900810095-2.5132882363-9.962980693033.785300526574.373887765332.0001731448-0.331628895629-0.669141038286-0.1306654337710.2807329086420.202529490795-0.276682047420.678433752720.6304355023420.117657683490.230076663755-0.0696857219167-0.05678152591010.2991114839840.03402699726230.2703559071362.57332410638-24.16783303529.37505671376
176.33127372983-1.671810737885.764562074353.21914604985-0.7276358685672.00040846698-0.4909874254130.7492903743950.402974291954-0.346473446017-0.0233658613647-0.324296777058-0.275130750980.2728992043610.5161781676660.299119537406-0.1481328510310.05193482668450.3563144374520.04647764565070.27858274370621.7217198809-8.42785241343-9.91784006836
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -3 through 3 )AA-3 - 31 - 7
22chain 'A' and (resid 4 through 10 )AA4 - 108 - 14
33chain 'A' and (resid 11 through 24 )AA11 - 2415 - 28
44chain 'A' and (resid 25 through 35 )AA25 - 3529 - 39
55chain 'A' and (resid 36 through 56 )AA36 - 5640 - 60
66chain 'A' and (resid 57 through 67 )AA57 - 6761 - 71
77chain 'A' and (resid 68 through 117 )AA68 - 11772 - 121
88chain 'B' and (resid -3 through 3 )BB-3 - 31 - 7
99chain 'B' and (resid 4 through 10 )BB4 - 108 - 14
1010chain 'B' and (resid 11 through 24 )BB11 - 2415 - 28
1111chain 'B' and (resid 25 through 35 )BB25 - 3529 - 39
1212chain 'B' and (resid 36 through 47 )BB36 - 4740 - 51
1313chain 'B' and (resid 48 through 67 )BB48 - 6752 - 71
1414chain 'B' and (resid 68 through 110 )BB68 - 11072 - 114
1515chain 'B' and (resid 111 through 117 )BB111 - 117115 - 121
1616chain 'C' and (resid 235 through 245 )CC235 - 2451 - 11
1717chain 'D' and (resid 235 through 245 )DD235 - 2451 - 11

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