[English] 日本語
Yorodumi
- PDB-7zkr: Human GABARAP in complex with stapled peptide Pen3-ortho -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zkr
TitleHuman GABARAP in complex with stapled peptide Pen3-ortho
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Pen3-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 / 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 / beta-tubulin binding / protein targeting / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ORTHO-XYLENE / PHOSPHATE ION / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)US, 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 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: Pen3-ortho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0227
Polymers15,5962
Non-polymers4275
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.030, 99.030, 99.030
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
Components on special symmetry positions
IDModelComponents
11B-101-

CL

21B-209-

HOH

-
Components

-
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 Pen3-ortho


Mass: 1509.726 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: residues (NH2) and (OXE) are not matched although they are present in coordinate file. Please check.
Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 211 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesium acetate, sodium cacodylate, PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.1→70.02 Å / Num. obs: 65281 / % possible obs: 100 % / Redundancy: 17.77 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.132 / Net I/σ(I): 11.48
Reflection shellResolution: 1.1→1.13 Å / Mean I/σ(I) obs: 1.38 / Num. unique obs: 4816 / CC1/2: 0.559 / Rrim(I) all: 1.694

-
Processing

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

3d32


Resolution: 1.1→49.51 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / Phase error: 16.8494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.167 3265 5 %
Rwork0.14 62012 -
obs0.1413 65277 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.32 Å2
Refinement stepCycle: LAST / Resolution: 1.1→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 25 206 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461375
X-RAY DIFFRACTIONf_angle_d0.79041881
X-RAY DIFFRACTIONf_chiral_restr0.0859187
X-RAY DIFFRACTIONf_plane_restr0.0122248
X-RAY DIFFRACTIONf_dihedral_angle_d12.7537524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.120.39131400.35072657X-RAY DIFFRACTION99.96
1.12-1.130.3041420.29512686X-RAY DIFFRACTION100
1.13-1.150.2361400.18842672X-RAY DIFFRACTION100
1.15-1.170.17961420.1712696X-RAY DIFFRACTION100
1.17-1.190.17161410.16512677X-RAY DIFFRACTION99.96
1.19-1.220.17211420.14572686X-RAY DIFFRACTION100
1.22-1.240.20081390.16242649X-RAY DIFFRACTION99.96
1.24-1.270.22141410.16962688X-RAY DIFFRACTION99.93
1.27-1.30.15841420.14392690X-RAY DIFFRACTION100
1.3-1.330.17751400.142663X-RAY DIFFRACTION100
1.33-1.370.16741420.12982694X-RAY DIFFRACTION100
1.37-1.410.16621410.13112685X-RAY DIFFRACTION100
1.41-1.450.15411420.11972687X-RAY DIFFRACTION100
1.45-1.50.15231420.11542701X-RAY DIFFRACTION100
1.5-1.560.13591420.1132699X-RAY DIFFRACTION99.96
1.56-1.640.14781400.1082668X-RAY DIFFRACTION100
1.64-1.720.12691430.1162706X-RAY DIFFRACTION100
1.72-1.830.16591420.13162708X-RAY DIFFRACTION100
1.83-1.970.15261430.13152704X-RAY DIFFRACTION99.89
1.97-2.170.1351420.12882701X-RAY DIFFRACTION100
2.17-2.480.16591430.13792729X-RAY DIFFRACTION99.93
2.48-3.130.17831440.14382737X-RAY DIFFRACTION100
3.13-49.510.17051500.14082829X-RAY DIFFRACTION99.9

+
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