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- PDB-7zl7: Human GABARAP in complex with stapled peptide Pen8-ortho -

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Basic information

Entry
Database: PDB / ID: 7zl7
TitleHuman GABARAP in complex with stapled peptide Pen8-ortho
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Pen8-ortho
KeywordsPROTEIN BINDING / Autophagy-related protein / stapled peptide / GABARAP / Inhibitor
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 / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding ...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 / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / protein targeting / sperm midpiece / autophagosome / microtubule cytoskeleton organization / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ORTHO-XYLENE / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsUeffing, A. / Brown, H. / Willbold, D. / Kritzer, J.A. / Weiergraeber, O.H.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM125856 United States
National Science Foundation (NSF, United States)2003010 United States
German Research Foundation (DFG)267205415 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy.
Authors: Brown, H. / Chung, M. / Uffing, A. / Batistatou, N. / Tsang, T. / Doskocil, S. / Mao, W. / Willbold, D. / Bast Jr., R.C. / Lu, Z. / Weiergraber, O.H. / Kritzer, J.A.
History
DepositionApr 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: Pen8-ortho
C: Gamma-aminobutyric acid receptor-associated protein
B: Pen8-ortho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,71115
Polymers31,1924
Non-polymers51911
Water5,873326
1
A: Gamma-aminobutyric acid receptor-associated protein
B: Pen8-ortho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8678
Polymers15,5962
Non-polymers2716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Pen8-ortho
C: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8447
Polymers15,5962
Non-polymers2485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.470, 72.420, 49.660
Angle α, β, γ (deg.)90.000, 100.042, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-204-

CL

21A-406-

HOH

31C-414-

HOH

41C-441-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACDB

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


Mass: 14086.176 Da / Num. of mol.: 2
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 Pen8-ortho


Mass: 1509.726 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: residues (NH2) and (OXE) are not matched although they are present in the coordinate file. Please check.
Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 337 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: sodium chloride, Tris-HCl, PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.55→49.35 Å / Num. obs: 33966 / % possible obs: 98.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.142 / Net I/σ(I): 6.01
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.34 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 2224 / CC1/2: 0.385 / Rrim(I) all: 1.164 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D32

3d32


Resolution: 1.55→49.35 Å / SU ML: 0.2458 / Cross valid method: FREE R-VALUE / Phase error: 24.3061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 1699 5 %
Rwork0.1743 32253 -
obs0.1766 33952 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.45 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 33 326 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682358
X-RAY DIFFRACTIONf_angle_d0.84683207
X-RAY DIFFRACTIONf_chiral_restr0.0603321
X-RAY DIFFRACTIONf_plane_restr0.0114420
X-RAY DIFFRACTIONf_dihedral_angle_d11.2712895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.43191270.35462408X-RAY DIFFRACTION88.79
1.6-1.650.31681370.30312602X-RAY DIFFRACTION94.94
1.65-1.710.31541430.26472709X-RAY DIFFRACTION99.58
1.71-1.770.27641420.23132702X-RAY DIFFRACTION99.34
1.77-1.860.23561430.21642723X-RAY DIFFRACTION99.62
1.86-1.950.27781430.21422702X-RAY DIFFRACTION99.03
1.95-2.080.2221450.16682761X-RAY DIFFRACTION99.38
2.08-2.240.23971410.1742680X-RAY DIFFRACTION99.37
2.24-2.460.23651440.17552730X-RAY DIFFRACTION99.1
2.46-2.820.23451440.17582727X-RAY DIFFRACTION99.72
2.82-3.550.17921450.15152764X-RAY DIFFRACTION99.39
3.55-49.350.16641450.13162745X-RAY DIFFRACTION98.23
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)
10.1937352453140.3589104921430.2056312045830.9464892471070.1715770902990.353667841003-0.01324310425450.00709131093297-0.0044770303183-0.125601728830.0392030034461-0.058938686505-0.0267786906130.04209660727532.17846852376E-80.1495262882950.003371590609340.006856876347620.158437182861-0.008520701647830.14776611834723.563020774167.436670360713.1170440994
20.318626831640.2749546872540.103578253461.11037724432-0.45774189430.3667270229380.000670468317848-0.0210949075741-0.10976067498-0.1089731231180.01947987763430.06087774846810.0618171708387-0.0246684554121-2.29174700597E-80.1513532468680.004374387526630.003864175443620.1517930006570.001951793296890.15096007634523.072025832336.493511827213.6509484657
30.4253297528110.00982725629158-0.1728989616560.07416370290580.04700188433110.1062852566660.06116139805460.0619006168867-0.0499131136851-0.1649183487490.1745103412680.07261325515080.288221626271-0.05275781769580.1451236850610.378642128-0.0717172818631-0.08447060432340.2085824362660.01059931708950.1621294552521.976059974728.75610865461.8162480937
40.0268611367706-0.01322401102410.01856180271780.01883755822780.009020728274010.0387328794102-0.1457750547170.1875025351850.0833838347247-0.2514516409180.1802732049980.00642416544855-0.210456939643-0.1444445944710.002544072666630.274628331030.00883548834962-0.05595785204130.2067185727710.0007361708157640.19675577998215.565454539375.13983882774.52075226479
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 117 )AA-1 - 1171 - 119
22chain 'C' and (resid -1 through 117 )CK-1 - 1171 - 119
33chain 'B' and (resid 0 through 101 )BG - J0 - 101
44chain 'D' and (resid 0 through 101 )DP - S0 - 101

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