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- PDB-7lk3: Crystal structure of untwinned human GABARAPL2 -

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Basic information

Entry
Database: PDB / ID: 7lk3
TitleCrystal structure of untwinned human GABARAPL2
ComponentsGamma-aminobutyric acid receptor-associated protein-like 2
KeywordsSIGNALING PROTEIN / autophagy / autophagosome / atg8 family / ubiquitin-like
Function / homology
Function and homology information


negative regulation of proteasomal protein catabolic process / protein localization to endoplasmic reticulum / GABA receptor binding / intra-Golgi vesicle-mediated transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / TBC/RABGAPs / Macroautophagy / beta-tubulin binding ...negative regulation of proteasomal protein catabolic process / protein localization to endoplasmic reticulum / GABA receptor binding / intra-Golgi vesicle-mediated transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / TBC/RABGAPs / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / SNARE binding / autophagy / protein transport / ATPase binding / cytoplasmic vesicle / microtubule binding / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScicluna, K. / Dewson, G. / Czabotar, P.E. / Birkinshaw, R.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: A new crystal form of GABARAPL2.
Authors: Scicluna, K. / Dewson, G. / Czabotar, P.E. / Birkinshaw, R.W.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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 2
B: Gamma-aminobutyric acid receptor-associated protein-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1293
Polymers28,0662
Non-polymers621
Water2,666148
1
A: Gamma-aminobutyric acid receptor-associated protein-like 2


Theoretical massNumber of molelcules
Total (without water)14,0331
Polymers14,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0952
Polymers14,0331
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.402, 58.700, 67.997
Angle α, β, γ (deg.)90.000, 98.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 2 / GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General ...GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General protein transport factor p16 / Golgi-associated ATPase enhancer of 16 kDa / GATE-16 / MAP1 light chain 3-related protein


Mass: 14033.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL2, FLC3A, GEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60520
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KBr, 30% (w/v) PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→33.65 Å / Num. obs: 17461 / % possible obs: 99.58 % / Redundancy: 7 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.9293 / Net I/σ(I): 14.55
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.9177 / Mean I/σ(I) obs: 2 / Num. unique obs: 1693 / CC1/2: 0.806 / CC star: 0.945 / Rrim(I) all: 0.9881 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4co7

4co7


Resolution: 1.9→33.65 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1764 -
Rwork0.1958 15741 -
obs-17445 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.48 Å2 / Biso mean: 32.7152 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 1.9→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 10 148 2096
Biso mean--45.32 35.86 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.34131360.30351155129198
1.95-2.010.31381480.254911991347100
2.01-2.070.29381150.23811205132098
2.07-2.140.26221340.217412031337100
2.14-2.230.26961440.22961192133699
2.23-2.330.29661210.21312391360100
2.33-2.450.26781420.21331176131899
2.45-2.610.23331310.21161242137399
2.61-2.810.23241370.213712191356100
2.81-3.090.26951410.21112131354100
3.09-3.540.2151350.185112241359100
3.54-4.460.17551360.159512151351100
4.46-44.230.19521440.180112591403100
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)
13.81412.4109-1.00984.35230.87613.63880.1183-1.0537-0.37280.9415-0.1504-0.42020.3835-0.0884-0.12550.46360.0044-0.05840.29080.02690.2876-2.3423-12.9496-23.521
22.78371.23010.20142.73130.72053.79460.0743-0.05030.0109-0.02740.04060.04560.1871-0.2626-0.0150.1766-0.01-0.00090.1915-0.01690.2692-9.3347-7.7098-34.4169
32.0738-0.5775-0.46789.37622.17474.58940.0803-0.979-0.26711.0582-0.0188-0.2410.74750.0735-0.1780.3060.0087-0.00620.4663-0.02020.2348-0.2992-0.4806-17.7446
41.86770.38860.37614.49521.8623.388-0.07690.010.0682-0.24640.0646-0.3189-0.1810.10410.02280.1574-0.02360.02710.1864-0.0210.32810.75194.4184-30.1215
51.86861.67330.38622.60470.66481.04280.00260.0177-0.2375-0.09590.194-0.40450.12760.3721-0.12420.16170.02250.01030.2381-0.04080.27454.3109-4.7101-28.2272
68.21935.922-0.43614.7198-0.36773.81180.3407-0.57730.89641.0365-0.07220.55780.12630.0721-0.27680.44770.01550.06880.2506-0.01910.4379-7.337313.984110.1503
72.26621.054-0.41484.8443-0.9524.44520.05490.14440.2467-0.26020.04290.0393-0.08880.0026-0.09550.18-0.00610.02150.19560.02350.2337-0.02249.2275-0.863
82.74080.381-1.19363.9189-1.64924.3916-0.1226-0.001-0.4152-0.0849-0.0136-0.1430.04060.03210.13420.1546-0.0044-0.00180.2327-0.01320.3741-8.2053-3.50188.902
93.31411.1739-2.08343.6279-0.23084.3439-0.14491.00380.1261-0.79020.32411.1285-0.1389-0.6126-0.00110.3619-0.0779-0.15010.40690.01680.4313-13.87991.6281-3.4038
103.85780.00110.17121.32450.52680.21880.09430.37610.26980.06920.20820.4102-0.1681-0.4322-0.17440.18810.0495-0.01860.26850.04390.3087-13.7185.93855.0321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )A0 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 35 )A11 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 47 )A36 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 98 )A48 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 117 )A99 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 10 )B0 - 10
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 35 )B11 - 35
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 79 )B36 - 79
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 98 )B80 - 98
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 117 )B99 - 117

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