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- PDB-9hgd: Crystal structure of human GABARAP in complex with cyclic peptide... -

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Basic information

Entry
Database: PDB / ID: 9hgd
TitleCrystal structure of human GABARAP in complex with cyclic peptide GAB_D23
Components
  • GAB_D23
  • Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN BINDING / autophagy-related protein / cyclic 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / protein targeting / smooth endoplasmic reticulum / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / 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
TRIETHYLENE GLYCOL / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUeffing, A. / Wilms, 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

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: GAB_D23
C: Gamma-aminobutyric acid receptor-associated protein
D: GAB_D23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,88910
Polymers31,1564
Non-polymers7346
Water2,846158
1
A: Gamma-aminobutyric acid receptor-associated protein
B: GAB_D23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7995
Polymers15,5782
Non-polymers2213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-24 kcal/mol
Surface area7650 Å2
MethodPISA
2
C: Gamma-aminobutyric acid receptor-associated protein
D: GAB_D23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0905
Polymers15,5782
Non-polymers5133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-3 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.630, 43.790, 67.520
Angle α, β, γ (deg.)90.000, 128.378, 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
11B-107-

HOH

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Components

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

#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 BL21(DE3) (bacteria) / References: UniProt: O95166
#2: Protein/peptide GAB_D23


Mass: 1491.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: cyclic peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 164 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES pH 5, 30% PEG 6000

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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
ReflectionResolution: 1.5→20.02 Å / Num. obs: 39046 / % possible obs: 97 % / Redundancy: 6.85 % / Biso Wilson estimate: 24.39 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.067 / Net I/σ(I): 13.34
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6.62 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 2844 / CC1/2: 0.346 / Rrim(I) all: 3.389 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18.42 Å / SU ML: 0.2385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1949 5 %
Rwork0.1878 37000 -
obs0.1896 38949 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.25 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 35 158 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572637
X-RAY DIFFRACTIONf_angle_d0.83573595
X-RAY DIFFRACTIONf_chiral_restr0.0804363
X-RAY DIFFRACTIONf_plane_restr0.0086481
X-RAY DIFFRACTIONf_dihedral_angle_d13.55371027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.4351350.42552550X-RAY DIFFRACTION94.18
1.54-1.580.38821360.36762595X-RAY DIFFRACTION95.12
1.58-1.630.33351380.32652621X-RAY DIFFRACTION97.49
1.63-1.680.29411390.30572633X-RAY DIFFRACTION97.57
1.68-1.740.32031370.26842594X-RAY DIFFRACTION97.33
1.74-1.810.27571380.24562629X-RAY DIFFRACTION97.16
1.81-1.890.2881380.21572622X-RAY DIFFRACTION95.83
1.89-1.990.25211370.19942601X-RAY DIFFRACTION97.68
1.99-2.110.22581420.1912678X-RAY DIFFRACTION97.92
2.11-2.280.22241400.1862669X-RAY DIFFRACTION98.84
2.28-2.50.21521400.18462657X-RAY DIFFRACTION97.29
2.51-2.870.22261420.18442688X-RAY DIFFRACTION99.05
2.87-3.610.19061420.16562701X-RAY DIFFRACTION97.63
3.61-18.420.1941450.15622762X-RAY DIFFRACTION98.28
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)
19.05794158142-2.05661783732-1.730336842635.844945784052.318559091165.95256783168-0.652991966248-0.507164553415-0.4980351429880.8068943981690.5145276306921.129715482940.526897074975-0.9268261139030.1019620205430.294269604970.03832981944970.03001023108590.3577449042920.03815950736680.4365814501730.931484968223-8.9136506828824.1860937186
22.018532376270.0142340213340.1627438125114.02574310101-2.005939284994.468573600530.05390280792660.131693240395-0.1092431338180.176539447917-0.161633663796-0.217789377176-0.1223805588870.6551065597540.1158595733950.1449462434150.0254204052119-0.008172636705350.261432609322-0.0378556478410.2166471349778.023685942512.6979819629420.3989771588
37.141576318273.723533821613.222051256314.90168149308-0.01692435879112.470335334540.2070883273690.367336701297-1.56971502386-0.239712340348-0.1204285974420.914909048140.117158120878-0.08957916239110.07804425336120.324615353130.0691023413805-0.02446301178730.323036951384-0.1648142610820.786399211718-5.38204376156-11.09991340713.0624352641
44.5668075129-0.662336202185-0.1005557122773.26099840151-1.220515137172.175720870810.02302836987780.482988186157-0.160323549764-0.302077040892-6.14105300113E-50.2851460262660.144752389717-0.257599143998-0.005541278173150.182240480637-0.00429589358394-0.04695217191520.33680990986-0.02541390462740.19253739953-7.847040505331.8463019017812.3524645769
56.495248733041.435671365493.023894308382.847697443340.93628961414.450716066960.299669050783-0.376440164246-0.6770803279450.243363464763-0.09158856604510.3765532061450.274972985528-0.440025519815-0.1749575496470.1607751157620.00292127938661-0.009236289881130.2549290974570.01336786736430.33212618501-6.28613975792-3.0515883960620.7153273014
63.864272498870.0540118894645-3.613854043.544930010650.003484576552743.386923475240.4768393868271.228267022580.397775948438-0.589454348088-0.302264285215-0.5104477806940.02511158005412.18220253795-0.2100443885240.368917904390.06763251812950.07128780163480.76705939088-0.02021302869940.3247455511947.396170588451.753040158658.15159369097
76.40097875219-6.215102933826.332164102066.1342029524-6.133968244736.31418646312-1.06152432332-2.52293657957-0.3282096270682.829058926891.027370419420.168131895325-1.06942375631-1.558540900410.2459152368630.7089055754610.08326204383910.04814124289350.606190178969-0.01003593632370.407292247976-33.57445620317.8854245143619.377652891
82.221835400652.61579535673-0.7249109370186.29828229102-5.081742031095.917791678710.4940798341940.7412611985521.27516052998-0.153495854146-0.341251678426-0.752480757402-0.1596524057530.137059311157-0.2100356050060.3165108044050.1177019639840.07768230281680.3817239834410.02103565776420.435555178282-42.836956510810.918875332612.3017215786
92.90664131528-1.5900692212-1.241020264066.859055660665.470880004916.873818950870.00187062408430.1496334812680.0301512190424-0.238788253306-0.2241513743990.217820712057-0.149589397373-0.817554229790.3102344768650.2186374697940.00201914427027-0.02319229549520.4421667662030.001240600897670.242618133334-49.0881046338-0.61506121416910.6982983696
105.875396922682.139469378660.4638963580433.752394112790.3896675581413.51997357422-0.1584566480050.5917982708060.115917732784-0.159059408006-0.06502868308470.139158485248-0.0798282445919-0.188289877820.2472568530810.154041066430.0201647945892-0.007323141727540.330755369053-0.001885165305360.134753769571-33.56112466150.1122356851386.81209594259
117.89016981827-1.877614247013.208355904696.88201945343-6.184623394096.89107787589-0.165547297460.925022808229-0.180754724431-0.0794437821410.07217215138940.0861368014802-0.0955780196333-0.2029264457040.1247909349930.2640345032960.01569850605210.03987559926680.457404311105-0.01729817198260.217606757101-24.9174889121-1.367263394043.94261449078
120.0695410675648-0.2436231064820.01758374124241.609794495950.4191245524120.147561564275-0.09380803004241.404358758320.758140530509-0.4123214040430.0740720583030.01430849152740.0293909801663-0.0827195932502-0.03267418246990.268012549306-0.01730006781920.008179988191820.7388102756390.1622594150080.299727802242-19.8685383354.643712162037.87189600856
139.741692002132.293807062890.7871996637273.041174142290.07895314918112.694725874-0.191956440847-0.176495164391-0.892214332361-0.01865577327640.139088966466-0.1907604615590.134447733539-0.04029588223210.04428577208980.1965420143820.003886754372460.007485516556090.2439190836260.01959286725340.258538226937-30.3317323272-7.0353465721116.6635995808
147.61447993143-4.604959913311.948286320613.44931902406-3.484805426399.36975602916-0.1656899178990.006716036258490.1399642134150.246136381130.072579136048-0.156790669123-0.483561960480.199161236860.0889064419260.212179818318-0.0204121749535-0.009149466011370.37595586885-0.06670862859740.260508096678-42.8414563355-1.7461593128916.2808878069
154.953364869970.0252581549868-1.130857903793.52302273739-0.7356977025114.22992330416-0.0749816228905-0.2082921501260.7605206443270.12455460983-0.115097805892-0.0666290089025-0.3516430704450.3249636165920.1910613255450.1992950009610.00579792141053-0.01468235795350.2597648020820.01444647392080.252941802548-25.77486222196.2783735026915.3088828619
163.395946161571.33885015149-3.648262074592.37945595130.783640434566.659226934120.2173698843232.13667993686-0.240551692743-1.02111950945-0.3646270257810.177128373425-0.381463794550.2453369615180.1538806160210.5801443075970.108971549025-0.01907414780390.778050831509-0.02223136521460.278050685968-39.7896275493-1.09980401594-1.32349985847
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 10 )AA-1 - 101 - 12
22chain 'A' and (resid 11 through 35 )AA11 - 3513 - 37
33chain 'A' and (resid 36 through 47 )AA36 - 4738 - 49
44chain 'A' and (resid 48 through 98 )AA48 - 9850 - 100
55chain 'A' and (resid 99 through 117 )AA99 - 117101 - 119
66chain 'B' and (resid 1 through 13 )BE1 - 131 - 13
77chain 'C' and (resid -1 through 3 )CF-1 - 31 - 5
88chain 'C' and (resid 4 through 10 )CF4 - 106 - 12
99chain 'C' and (resid 11 through 24 )CF11 - 2413 - 26
1010chain 'C' and (resid 25 through 56 )CF25 - 5627 - 58
1111chain 'C' and (resid 57 through 68 )CF57 - 6859 - 70
1212chain 'C' and (resid 69 through 80 )CF69 - 8071 - 82
1313chain 'C' and (resid 81 through 98 )CF81 - 9883 - 100
1414chain 'C' and (resid 99 through 104 )CF99 - 104101 - 106
1515chain 'C' and (resid 105 through 117 )CF105 - 117107 - 119
1616chain 'D' and (resid 1 through 13 )DJ1 - 131 - 13

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