[English] 日本語
Yorodumi
- PDB-5azg: Crystal structure of LGG-1 complexed with a UNC-51 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5azg
TitleCrystal structure of LGG-1 complexed with a UNC-51 peptide
Components
  • Protein lgg-1
  • Serine/threonine-protein kinase unc-51
KeywordsPROTEIN BINDING / autophagy / ubiquitin-like
Function / homology
Function and homology information


TBC/RABGAPs / Receptor Mediated Mitophagy / dauer larval development / Macroautophagy / nematode male tail tip morphogenesis / cellular response to toxic substance / positive regulation of autophagosome assembly / xenophagy / autophagy of mitochondrion / GABA receptor binding ...TBC/RABGAPs / Receptor Mediated Mitophagy / dauer larval development / Macroautophagy / nematode male tail tip morphogenesis / cellular response to toxic substance / positive regulation of autophagosome assembly / xenophagy / autophagy of mitochondrion / GABA receptor binding / programmed cell death / plasma membrane repair / cellular response to nitrogen starvation / phagophore assembly site / regulation of axon extension / apoptotic cell clearance / embryo development ending in birth or egg hatching / regulation of cell size / autophagosome membrane / necroptotic process / autophagosome assembly / regulation of multicellular organism growth / autophagosome / lysosomal lumen / axonogenesis / axon guidance / determination of adult lifespan / macroautophagy / autophagy / phagocytic vesicle membrane / regulation of protein localization / cell migration / response to heat / perikaryon / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / defense response to Gram-positive bacterium / axon / protein phosphorylation / protein serine/threonine kinase activity / dendrite / neuronal cell body / ubiquitin protein ligase binding / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Unc-51 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Serine/threonine-protein kinase Unc-51 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
: / Protein lgg-1 / Serine/threonine-protein kinase unc-51
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsWatanabe, Y. / Fujioka, Y. / Noda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan25111004 Japan
Japan Science and Technology AgencyCREST Japan
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy.
Authors: Wu, F. / Watanabe, Y. / Guo, X.Y. / Qi, X. / Wang, P. / Zhao, H.Y. / Wang, Z. / Fujioka, Y. / Zhang, H. / Ren, J.Q. / Fang, T.C. / Shen, Y.X. / Feng, W. / Hu, J.J. / Noda, N.N. / Zhang, H.
History
DepositionOct 5, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed ..._citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein lgg-1
B: Protein lgg-1
C: Serine/threonine-protein kinase unc-51
D: Serine/threonine-protein kinase unc-51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,63318
Polymers31,0594
Non-polymers1,57414
Water1,928107
1
A: Protein lgg-1
C: Serine/threonine-protein kinase unc-51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,42910
Polymers15,5302
Non-polymers8998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-33 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: Protein lgg-1
D: Serine/threonine-protein kinase unc-51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2048
Polymers15,5302
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-42 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.684, 80.116, 111.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Protein lgg-1


Mass: 14279.358 Da / Num. of mol.: 2 / Fragment: UNP residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lgg-1, C32D5.9 / Plasmid: pGEX-6P / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q09490
#2: Protein/peptide Serine/threonine-protein kinase unc-51 / UNC-51 AIM


Mass: 1250.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: Q23023
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTyr was added to the N-terminus of UNC-51 LIR for quantification.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, cadmium chloride

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→55.8 Å / Num. obs: 26489 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.878 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AZF

5azf


Resolution: 1.81→55.75 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.646 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24608 1288 4.9 %RANDOM
Rwork0.21171 ---
obs0.21339 25170 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å2-0 Å2
2--0.54 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.81→55.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 14 107 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192173
X-RAY DIFFRACTIONr_bond_other_d0.0020.022070
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9662928
X-RAY DIFFRACTIONr_angle_other_deg0.88434770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93923.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2881516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3053.142992
X-RAY DIFFRACTIONr_mcbond_other1.3053.141991
X-RAY DIFFRACTIONr_mcangle_it2.0744.6991233
X-RAY DIFFRACTIONr_mcangle_other2.0734.71234
X-RAY DIFFRACTIONr_scbond_it1.6083.4121181
X-RAY DIFFRACTIONr_scbond_other1.6083.4131181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7165.0241695
X-RAY DIFFRACTIONr_long_range_B_refined5.50125.5322443
X-RAY DIFFRACTIONr_long_range_B_other5.19125.0792390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.806→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 97 -
Rwork0.252 1768 -
obs--96.53 %
Refinement TLS params.Method: refined / Origin x: 12.428 Å / Origin y: 16.537 Å / Origin z: 13.041 Å
111213212223313233
T0.2005 Å20.0245 Å20.0245 Å2-0.1752 Å2-0.0582 Å2--0.0306 Å2
L2.183 °20.483 °20.4234 °2-2.6731 °20.2262 °2--2.2825 °2
S-0.0132 Å °-0.5787 Å °0.2148 Å °0.6431 Å °-0.0542 Å °0.1802 Å °-0.2033 Å °-0.0031 Å °0.0675 Å °

+
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