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- PDB-9i9x: Human GABARAP in complex with artificial peptide IM-2 -

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Basic information

Entry
Database: PDB / ID: 9i9x
TitleHuman GABARAP in complex with artificial peptide IM-2
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • artificial peptide IM-2
KeywordsPROTEIN BINDING / GABARAP / artificial peptide / autophagy-related protein / ATG8
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome maturation / axoneme / protein targeting / autophagosome assembly / beta-tubulin binding / mitophagy / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / sperm midpiece / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWilms, J.A. / McDonald, I. / Willbold, D. / Kritzer, J.A. / Weiergraeber, O.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)267205415-SFB 1208 Germany
CitationJournal: To Be Published
Title: Human GABARAP in complex with artificial peptide IM-2
Authors: McDonald, I. / Wilms, J.A. / Weiergraeber, O.H. / Kritzer, J.A.
History
DepositionFeb 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: 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
B: artificial peptide IM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7569
Polymers15,1132
Non-polymers6437
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-33 kcal/mol
Surface area7490 Å2
Unit cell
Length a, b, c (Å)101.340, 101.340, 101.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14086.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: O95166
#2: Protein/peptide artificial peptide IM-2


Mass: 1027.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 220 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, sodium cacodylate trihydrate, PEG 8000, DMSO, Tris-HCl, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.42→41.37 Å / Num. all: 32718 / Num. obs: 32718 / % possible obs: 100 % / Redundancy: 13.84 % / Biso Wilson estimate: 28.18 Å2 / CC1/2: 1 / Rrim(I) all: 0.071 / Net I/σ(I): 20.49
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 14.13 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2386 / CC1/2: 0.3 / Rrim(I) all: 2.824 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→41.37 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1636 5 %
Rwork0.1735 31082 -
obs0.1747 32718 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 1.42→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 38 214 1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611361
X-RAY DIFFRACTIONf_angle_d0.85621855
X-RAY DIFFRACTIONf_chiral_restr0.0833188
X-RAY DIFFRACTIONf_plane_restr0.0082248
X-RAY DIFFRACTIONf_dihedral_angle_d12.5677531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.32671360.30572586X-RAY DIFFRACTION100
1.46-1.510.31141330.27432541X-RAY DIFFRACTION100
1.51-1.560.2151350.24352557X-RAY DIFFRACTION100
1.56-1.630.24431360.22282590X-RAY DIFFRACTION100
1.63-1.70.24821350.21132551X-RAY DIFFRACTION100
1.7-1.790.19651360.1912586X-RAY DIFFRACTION100
1.79-1.90.22711350.19292565X-RAY DIFFRACTION100
1.9-2.050.1911370.17992604X-RAY DIFFRACTION100
2.05-2.250.19991360.17732593X-RAY DIFFRACTION100
2.25-2.580.19851370.17722597X-RAY DIFFRACTION100
2.58-3.250.24141380.16822622X-RAY DIFFRACTION100
3.25-41.370.14731420.14152690X-RAY DIFFRACTION99.93

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