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- PDB-7jhx: Crystal structure of hEPG5 LIR/GABARAPL1 complex -

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Basic information

Entry
Database: PDB / ID: 7jhx
TitleCrystal structure of hEPG5 LIR/GABARAPL1 complex
Components
  • Ectopic P granules protein 5 homolog
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


nucleotide transport / cellular response to dsDNA / glycophagy / Tat protein binding / GABA receptor binding / toll-like receptor 9 signaling pathway / cellular response to nitrogen starvation / phosphatidylethanolamine binding / endocytic recycling / Macroautophagy ...nucleotide transport / cellular response to dsDNA / glycophagy / Tat protein binding / GABA receptor binding / toll-like receptor 9 signaling pathway / cellular response to nitrogen starvation / phosphatidylethanolamine binding / endocytic recycling / Macroautophagy / endosome to lysosome transport / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / autophagy / microtubule / lysosome / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Ectopic P granules protein 5 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein-like 1 / Ectopic P granules protein 5 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCheung, Y.W.S. / Yip, C.K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Commun Biol / Year: 2021
Title: Insights on autophagosome-lysosome tethering from structural and biochemical characterization of human autophagy factor EPG5.
Authors: Sung-Eun Nam / Yiu Wing Sunny Cheung / Thanh Ngoc Nguyen / Michael Gong / Samuel Chan / Michael Lazarou / Calvin K Yip /
Abstract: Pivotal to the maintenance of cellular homeostasis, macroautophagy (hereafter autophagy) is an evolutionarily conserved degradation system that involves sequestration of cytoplasmic material into the ...Pivotal to the maintenance of cellular homeostasis, macroautophagy (hereafter autophagy) is an evolutionarily conserved degradation system that involves sequestration of cytoplasmic material into the double-membrane autophagosome and targeting of this transport vesicle to the lysosome/late endosome for degradation. EPG5 is a large-sized metazoan protein proposed to serve as a tethering factor to enforce autophagosome-lysosome/late endosome fusion specificity, and its deficiency causes a severe multisystem disorder known as Vici syndrome. Here, we show that human EPG5 (hEPG5) adopts an extended "shepherd's staff" architecture. We find that hEPG5 binds preferentially to members of the GABARAP subfamily of human ATG8 proteins critical to autophagosome-lysosome fusion. The hEPG5-GABARAPs interaction, which is mediated by tandem LIR motifs that exhibit differential affinities, is required for hEPG5 recruitment to mitochondria during PINK1/Parkin-dependent mitophagy. Lastly, we find that the Vici syndrome mutation Gln336Arg does not affect the hEPG5's overall stability nor its ability to engage in interaction with the GABARAPs. Collectively, results from our studies reveal new insights into how hEPG5 recognizes mature autophagosome and establish a platform for examining the molecular effects of Vici syndrome disease mutations on hEPG5.
History
DepositionJul 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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: Ectopic P granules protein 5 homolog
D: Ectopic P granules protein 5 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1107
Polymers31,8224
Non-polymers2883
Water4,342241
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Ectopic P granules protein 5 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0073
Polymers15,9112
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-22 kcal/mol
Surface area6970 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
D: Ectopic P granules protein 5 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1034
Polymers15,9112
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-31 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.954, 33.082, 78.858
Angle α, β, γ (deg.)90.000, 114.280, 90.000
Int Tables number5
Space group name H-MC121

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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: 14479.526 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 Ectopic P granules protein 5 homolog


Mass: 1431.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HCE0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium sulfate, 0.1 MES buffer pH 5.5, 29% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.91→57 Å / Num. obs: 21346 / % possible obs: 93.4 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.097 / Rrim(I) all: 0.177 / Net I/σ(I): 4.6 / Num. measured all: 68435 / Scaling rejects: 52
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.91-1.960.76228679890.5990.5040.9161.658.7
8.54-570.0678432890.9850.0450.0818.999

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2Q

2r2q


Resolution: 1.91→57 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 999 4.72 %
Rwork0.1969 20185 -
obs0.1991 21184 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.14 Å2 / Biso mean: 25.4466 Å2 / Biso min: 8.26 Å2
Refinement stepCycle: final / Resolution: 1.91→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 15 241 2353
Biso mean--48.68 31.03 -
Num. residues----247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9101-2.01080.3021970.28197464
2.0108-2.13680.2661360.2416292394
2.1368-2.30180.27271520.2218298297
2.3018-2.53340.28891680.2267300497
2.5334-2.90.26051560.2051301097
2.9-3.65360.22341500.1809309398
3.6536-570.2111400.1638319998
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)
19.2432.3241-1.17055.10135.54527.7267-0.22280.7234-0.1688-1.3147-0.23360.2390.19870.31370.42990.2920.06350.00510.2625-0.00360.18537.4182-8.85639.6693
25.97191.83720.8158.23471.29842.1472-0.14880.39750.0173-0.27710.4786-0.0493-0.8829-0.4472-0.30530.29130.01340.01410.3823-0.01130.3736-13.027211.156712.6287
38.05670.0168-5.55317.32032.50777.25870.0518-1.02470.3837-0.39740.3553-1.0171-0.14781.0179-0.35880.16630.00870.05520.2247-0.03790.311824.253-6.490230.3803
43.9417-4.00510.15315.20441.86426.44880.2942-0.8143-0.56680.2383-0.05630.18010.7336-0.1231-0.19490.1659-0.0550.0060.29670.08360.2713-22.2198-4.184217.1929
53.83892.6376-3.04743.6218-5.09187.93070.14260.8570.5418-0.15230.04670.3059-0.23950.0646-0.08520.21280.0678-0.01080.4820.05780.2162-23.9083.39945.2269
65.8004-0.45571.36395.3202-2.77839.36680.09050.3640.6532-0.19730.22440-0.3632-0.2807-0.36130.11290.05130.06910.26610.02820.2427-13.26045.17389.7842
77.18420.68132.2613.64770.10397.3154-0.2465-0.889-0.34850.5820.28420.1887-0.0859-0.37550.01110.25050.02980.07660.2576-0.00370.1475-11.2208-0.641725.1404
83.8078-1.22691.31452.32410.05493.78520.00740.24820.2074-0.01660.00380.029-0.2565-0.030.01650.08930.00080.00490.12930.02410.1233-3.20341.900115.1489
95.7935-0.0669-1.71252.104-1.13662.3280.01160.6886-0.1983-0.0102-0.00220.18120.0763-0.3134-0.01470.14580.0322-0.03120.3102-0.01630.1308-13.3799-2.53084.0421
106.7158-2.34983.98091.3207-0.44144.6280.1216-0.4169-0.5033-0.01180.17410.07760.4633-0.5029-0.34690.1251-0.02070.02220.1890.04120.2095-7.5902-7.185119.7887
113.68382.66841.39387.2413.72881.98550.0460.8590.387-0.8382-0.20770.18220.19590.44620.18340.27270.07110.0380.27460.01950.150425.1587-16.135515.1449
124.4446-2.1009-3.48083.11972.95533.98-0.2149-0.317-0.07520.22770.0135-0.16880.11390.7230.20070.13170.0139-0.02260.15030.03220.154327.4199-20.505628.2316
133.4704-0.64451.03163.0784-2.34727.7965-0.14260.07910.10070.0058-0.0987-0.2225-0.04480.11830.19660.0483-0.009-0.0040.0754-0.00810.084719.5734-11.951928.1905
147.6199-1.57544.12178.1708-1.33247.1462-0.11990.72120.438-0.4788-0.0892-0.1404-0.0310.39050.19070.1386-0.01790.07830.17960.0420.144918.2226-4.495313.9627
155.2682-2.80131.18213.3341-2.0272.4147-0.09340.00090.03760.17950.0093-0.15740.0409-0.00360.08010.13150.0128-0.0320.1149-0.04760.072113.0499-5.359728.4794
165.6904-1.12421.30146.89232.42843.9426-0.02050.13820.5441-0.4072-0.0151-0.2925-0.35240.1880.01290.1239-0.0026-0.01960.13370.01410.10739.73370.325716.4991
175.6495-2.86743.50323.9063-0.24384.9591-0.0004-0.1237-0.39930.07080.11630.13740.234-0.1471-0.11390.0941-0.03530.02180.08180.00080.14618.4323-16.647625.804
185.0038-4.53132.58287.5115-5.26286.70840.0635-0.0922-0.2830.00550.04110.23150.27270.2485-0.07120.0789-0.013-0.01820.09-0.01520.092617.6229-17.485722.0981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 111 through 117 )B111 - 117
2X-RAY DIFFRACTION2chain 'C' and (resid 566 through 571 )C566 - 571
3X-RAY DIFFRACTION3chain 'D' and (resid 564 through 571 )D564 - 571
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 10 )A1 - 10
5X-RAY DIFFRACTION5chain 'A' and (resid 11 through 24 )A11 - 24
6X-RAY DIFFRACTION6chain 'A' and (resid 25 through 35 )A25 - 35
7X-RAY DIFFRACTION7chain 'A' and (resid 36 through 47 )A36 - 47
8X-RAY DIFFRACTION8chain 'A' and (resid 48 through 90 )A48 - 90
9X-RAY DIFFRACTION9chain 'A' and (resid 91 through 104 )A91 - 104
10X-RAY DIFFRACTION10chain 'A' and (resid 105 through 117 )A105 - 117
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 10 )B2 - 10
12X-RAY DIFFRACTION12chain 'B' and (resid 11 through 24 )B11 - 24
13X-RAY DIFFRACTION13chain 'B' and (resid 25 through 35 )B25 - 35
14X-RAY DIFFRACTION14chain 'B' and (resid 36 through 47 )B36 - 47
15X-RAY DIFFRACTION15chain 'B' and (resid 48 through 67 )B48 - 67
16X-RAY DIFFRACTION16chain 'B' and (resid 68 through 79 )B68 - 79
17X-RAY DIFFRACTION17chain 'B' and (resid 80 through 98 )B80 - 98
18X-RAY DIFFRACTION18chain 'B' and (resid 99 through 110 )B99 - 110

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