[English] 日本語
Yorodumi
- PDB-5lxi: GABARAP-L1 ATG4B LIR Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lxi
TitleGABARAP-L1 ATG4B LIR Complex
Components
  • Cysteine protease ATG4B
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / LIR / GABARAP / ATG8 / LC3
Function / homology
Function and homology information


otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / aggrephagy / glycophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / GABA receptor binding / Tat protein binding ...otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / aggrephagy / glycophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Macroautophagy / autophagosome membrane / autophagosome maturation / autophagosome assembly / beta-tubulin binding / mitophagy / cysteine-type peptidase activity / autophagosome / cytoplasmic vesicle membrane / macroautophagy / protein processing / phospholipid binding / autophagy / protein transport / cytoplasmic vesicle / scaffold protein binding / endopeptidase activity / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cilium / ciliary basal body / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / endoplasmic reticulum / Golgi apparatus / mitochondrion / proteolysis / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase C54 / Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / Peptidase C54 catalytic domain / ATG4, F-type LIR motif / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) ...Peptidase C54 / Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / Peptidase C54 catalytic domain / ATG4, F-type LIR motif / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PEROXIDE ION / TRIETHYLENE GLYCOL / Gamma-aminobutyric acid receptor-associated protein-like 1 / Cysteine protease ATG4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMouilleron, S. / Skytte Rasmussen, M. / Kumar Shrestha, B. / Wirth, M. / Bowitz Larsen, K. / Abudu Princely, Y. / Sjottem, E. / Tooze, S. / Lamark, T. / Johansen, T. / Lee, R.
CitationJournal: Autophagy / Year: 2017
Title: ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.
Authors: Skytte Rasmussen, M. / Mouilleron, S. / Kumar Shrestha, B. / Wirth, M. / Lee, R. / Bowitz Larsen, K. / Abudu Princely, Y. / O'Reilly, N. / Sjttem, E. / Tooze, S.A. / Lamark, T. / Johansen, T.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Cysteine protease ATG4B
E: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,38113
Polymers31,7764
Non-polymers6059
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.888, 72.377, 30.620
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules DBCE

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14598.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q9H0R8
#2: Protein/peptide Cysteine protease ATG4B / AUT-like 1 cysteine endopeptidase / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / ...AUT-like 1 cysteine endopeptidase / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / Autophagy-related protein 4 homolog B / hAPG4B


Mass: 1289.236 Da / Num. of mol.: 2 / Fragment: UNP residues 384-393 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9Y4P1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

-
Non-polymers , 6 types, 109 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.44→35 Å / Num. obs: 46217 / % possible obs: 96 % / Redundancy: 3.1 % / CC1/2: 0.998 / Rsym value: 0.038 / Net I/σ(I): 10.1
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.74 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r2q

2r2q


Resolution: 1.44→31.207 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2265 4.9 %
Rwork0.1969 --
obs0.1987 46205 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→31.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 38 100 2216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142252
X-RAY DIFFRACTIONf_angle_d1.1593056
X-RAY DIFFRACTIONf_dihedral_angle_d22.708875
X-RAY DIFFRACTIONf_chiral_restr0.101313
X-RAY DIFFRACTIONf_plane_restr0.008399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.47130.41771400.36372648X-RAY DIFFRACTION92
1.4713-1.50550.40551180.32852668X-RAY DIFFRACTION92
1.5055-1.54320.33811380.31022676X-RAY DIFFRACTION92
1.5432-1.58490.35631160.30142667X-RAY DIFFRACTION93
1.5849-1.63160.32421380.27532683X-RAY DIFFRACTION94
1.6316-1.68420.33451240.24872754X-RAY DIFFRACTION94
1.6842-1.74440.28061240.23422706X-RAY DIFFRACTION94
1.7444-1.81420.26441210.21922777X-RAY DIFFRACTION95
1.8142-1.89680.27091630.20012735X-RAY DIFFRACTION95
1.8968-1.99680.24851650.18952731X-RAY DIFFRACTION96
1.9968-2.12190.22951380.17722806X-RAY DIFFRACTION96
2.1219-2.28560.25961540.18322776X-RAY DIFFRACTION97
2.2856-2.51560.24531690.18962798X-RAY DIFFRACTION97
2.5156-2.87940.22921270.18992821X-RAY DIFFRACTION97
2.8794-3.62680.19421520.17552846X-RAY DIFFRACTION98
3.6268-31.21470.17171780.16442848X-RAY DIFFRACTION97

+
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