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- PDB-9hgc: Crystal structure of human GABARAPL1 in complex with cyclic pepti... -

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Basic information

Entry
Database: PDB / ID: 9hgc
TitleCrystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8
Components
  • GAB_D8
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsPROTEIN BINDING / autophagy-related protein / cyclic peptide / GABARAPL1 / inhibitor
Function / homology
Function and homology information


glycophagy / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Macroautophagy / autophagosome membrane / autophagosome assembly / autophagosome maturation / beta-tubulin binding ...glycophagy / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Macroautophagy / autophagosome membrane / autophagosome assembly / autophagosome maturation / beta-tubulin binding / mitophagy / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / microtubule / cilium / ciliary basal body / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / endoplasmic reticulum / Golgi apparatus / plasma membrane / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsWilms, J.A. / Willbold, D. / Weiergraeber, O.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)267205415 Germany
Citation
Journal: Nat.Chem.Biol. / Year: 2025
Title: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.
Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G.
#1: Journal: Biorxiv / Year: 2024
Title: Accurate de novo design of high-affinity protein binding macrocycles using deep learning.
Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: GAB_D8
C: Gamma-aminobutyric acid receptor-associated protein-like 1
D: GAB_D8
E: Gamma-aminobutyric acid receptor-associated protein-like 1
F: GAB_D8
G: Gamma-aminobutyric acid receptor-associated protein-like 1
H: GAB_D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,12812
Polymers63,7528
Non-polymers3764
Water39622
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: GAB_D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0343
Polymers15,9382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Gamma-aminobutyric acid receptor-associated protein-like 1
D: GAB_D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers15,9382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Gamma-aminobutyric acid receptor-associated protein-like 1
F: GAB_D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0303
Polymers15,9382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Gamma-aminobutyric acid receptor-associated protein-like 1
H: GAB_D8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0343
Polymers15,9382
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.290, 116.810, 116.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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: 14212.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H0R8
#2: Protein/peptide
GAB_D8


Mass: 1725.718 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: cyclic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: -h,l,k / Fraction: 0.48
ReflectionResolution: 2.52→58.42 Å / Num. obs: 24336 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rrim(I) all: 0.238 / Net I/σ(I): 10.01
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 1803 / CC1/2: 0.291 / Rrim(I) all: 3.279 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→58.42 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1169 4.81 %
Rwork0.2147 23159 -
obs0.2337 24328 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.03 Å2
Refinement stepCycle: LAST / Resolution: 2.52→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 22 22 4522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164645
X-RAY DIFFRACTIONf_angle_d0.416278
X-RAY DIFFRACTIONf_chiral_restr0.041625
X-RAY DIFFRACTIONf_plane_restr0.0042824
X-RAY DIFFRACTIONf_dihedral_angle_d11.40441777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.630.32571490.32282847X-RAY DIFFRACTION94.3
2.63-2.770.39721420.32732845X-RAY DIFFRACTION94.9
2.77-2.950.34881600.31422837X-RAY DIFFRACTION94.32
2.95-3.170.35481480.29232867X-RAY DIFFRACTION94.81
3.17-3.490.30011350.25282862X-RAY DIFFRACTION94.96
3.49-40.30551260.22732934X-RAY DIFFRACTION95.17
4-5.040.22071570.17742900X-RAY DIFFRACTION94.13
5.04-58.420.23791430.21353076X-RAY DIFFRACTION94.7

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