[English] 日本語
Yorodumi
- PDB-9hgd: Crystal structure of human GABARAP in complex with cyclic peptide... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome maturation / protein targeting / beta-tubulin binding / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more