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- PDB-5yiq: Crystal structure of AnkG LIR/LC3B complex -

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Basic information

Entry
Database: PDB / ID: 5yiq
TitleCrystal structure of AnkG LIR/LC3B complex
Components
  • Ankyrin-3
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


Receptor Mediated Mitophagy / regulation of protein targeting / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / positive regulation of sodium ion import across plasma membrane / TBC/RABGAPs / membrane assembly / Macroautophagy / protein localization to axon ...Receptor Mediated Mitophagy / regulation of protein targeting / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / positive regulation of sodium ion import across plasma membrane / TBC/RABGAPs / membrane assembly / Macroautophagy / protein localization to axon / Pexophagy / positive regulation of mucus secretion / clustering of voltage-gated sodium channels / PINK1-PRKN Mediated Mitophagy / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / magnesium ion homeostasis / regulation of potassium ion transport / positive regulation of membrane potential / plasma membrane organization / mucus secretion / negative regulation of delayed rectifier potassium channel activity / channel activator activity / maintenance of protein location in cell / phosphorylation-dependent protein binding / positive regulation of homotypic cell-cell adhesion / paranode region of axon / positive regulation of sodium ion transport / regulation of modification of postsynaptic structure / negative regulation of endocytosis / axon initial segment / costamere / anterograde axonal transport / cellular response to magnesium ion / KEAP1-NFE2L2 pathway / Golgi to plasma membrane protein transport / node of Ranvier / spectrin binding / neuromuscular junction development / axon development / response to immobilization stress / autolysosome / mitotic cytokinesis / autophagosome membrane / intercalated disc / axoneme / lateral plasma membrane / sodium channel regulator activity / positive regulation of protein targeting to membrane / bicellular tight junction / neuronal action potential / mitophagy / cytoskeletal protein binding / axon cytoplasm / T-tubule / endomembrane system / axonogenesis / autophagosome / axon guidance / basal plasma membrane / sarcoplasmic reticulum / cellular response to starvation / protein localization to plasma membrane / neuromuscular junction / establishment of protein localization / establishment of localization in cell / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / sarcolemma / mitochondrial membrane / structural constituent of cytoskeleton / autophagy / Z disc / cytoplasmic vesicle / protein-macromolecule adaptor activity / basolateral plasma membrane / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / lysosome / postsynapse / neuron projection / postsynaptic density / cadherin binding / axon / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / cell surface / signal transduction / nucleus / membrane / plasma membrane
Similarity search - Function
Ankyrin-3, death domain / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like ...Ankyrin-3, death domain / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ankyrin-3 / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, J. / Zhu, R. / Chen, K. / Zheng, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council (RGC)AoE-M09-12 Hong Kong
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins.
Authors: Li, J. / Zhu, R. / Chen, K. / Zheng, H. / Zhao, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_special_symmetry
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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_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_symmetry / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
D: Ankyrin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8196
Polymers17,5582
Non-polymers2624
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-86 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.553, 64.553, 155.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14637.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map1lc3b, Map1alc3, Map1lc3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV6
#2: Protein/peptide Ankyrin-3 / ANK-3 / Ankyrin-G


Mass: 2919.998 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1985-2010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ank3 / Production host: Escherichia coli (E. coli) / References: UniProt: O70511
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6417 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.064 / Rrim(I) all: 0.149 / Χ2: 1.959 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.61.211.93100.5470.5631.3381.344100
2.64-2.695.313190.7060.4711.1081.517100
2.69-2.745.61.0782950.6670.4961.1891.452100
2.74-2.85.40.7693170.780.3620.8531.418100
2.8-2.865.60.7253020.8170.3380.8021.561100
2.86-2.935.40.6443220.8580.3030.7141.474100
2.93-35.50.4763040.9240.2220.5261.58499.7
3-3.085.50.4143130.9290.1930.4581.527100
3.08-3.175.40.323110.9570.150.3551.577100
3.17-3.285.40.2953080.9520.1390.3261.87100
3.28-3.395.40.213140.9820.0990.2331.912100
3.39-3.535.40.1823160.9790.0870.2022.098100
3.53-3.695.20.1443170.9880.0680.162.358100
3.69-3.885.20.1313210.9850.0630.1462.34100
3.88-4.135.10.0953240.9930.0450.1052.4899.7
4.13-4.455.10.0773230.9930.0370.0862.48899.7
4.45-4.894.90.0643300.9950.0310.0712.511100
4.89-5.65.10.0713390.9960.0330.0782.39899.7
5.6-7.0550.0783470.9940.0380.0872.685100
7.05-504.30.0483850.9980.0250.0552.77696

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UGM

1ugm


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.767 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.288
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 314 4.9 %RANDOM
Rwork0.2174 ---
obs0.2194 6052 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 148.88 Å2 / Biso mean: 53.855 Å2 / Biso min: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å2-0 Å2
3----1.97 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 4 9 1063
Biso mean--84.06 45.08 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0010.02980
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9511447
X-RAY DIFFRACTIONr_angle_other_deg0.9532253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05923.20853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76515184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1921510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 17 -
Rwork0.329 421 -
all-438 -
obs--94.6 %

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