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- PDB-5yip: Crystal Structure of AnkG LIR/GABARAPL1 complex -

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Basic information

Entry
Database: PDB / ID: 5yip
TitleCrystal Structure of AnkG LIR/GABARAPL1 complex
Components
  • Ankyrin-3
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / Autophagy
Function / homology
Function and homology information


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 / substrate localization to autophagosome / membrane assembly / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels ...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 / substrate localization to autophagosome / membrane assembly / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / magnesium ion homeostasis / regulation of potassium ion transport / positive regulation of membrane potential / glycophagy / plasma membrane organization / 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 / Tat protein binding / cellular response to magnesium ion / Golgi to plasma membrane protein transport / node of Ranvier / spectrin binding / neuromuscular junction development / axon development / response to immobilization stress / mitotic cytokinesis / intercalated disc / lateral plasma membrane / sodium channel regulator activity / positive regulation of protein targeting to membrane / bicellular tight junction / neuronal action potential / cytoskeletal protein binding / protein-membrane adaptor activity / axon cytoplasm / T-tubule / axonogenesis / autophagosome / axon guidance / basal plasma membrane / cytoplasmic vesicle membrane / sarcoplasmic reticulum / protein localization to plasma membrane / neuromuscular junction / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / sarcolemma / synapse organization / phospholipid binding / structural constituent of cytoskeleton / Z disc / protein-macromolecule adaptor activity / basolateral plasma membrane / microtubule / transmembrane transporter binding / RNA polymerase II-specific DNA-binding transcription factor binding / postsynaptic membrane / cytoskeleton / lysosome / postsynapse / neuron projection / postsynaptic density / ciliary basal body / cadherin binding / axon / dendrite / synapse / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / cell surface / endoplasmic reticulum / Golgi apparatus / signal transduction / mitochondrion / nucleus / membrane / plasma membrane / cytosol
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 / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / Category: citation
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Ankyrin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6553
Polymers17,5632
Non-polymers921
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-6 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.172, 104.172, 63.901
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

21A-357-

HOH

31B-2102-

HOH

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Components

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


Mass: 14642.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gabarapl1, Apg8l, Atg8l, Gec1, MNCb-0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R3R8
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 18077 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.022 / Rrim(I) all: 0.087 / Χ2: 0.529 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.85-1.8814.18980.8870.280.452100
1.88-1.9215.68660.8970.2290.4631000.8860.916
1.92-1.9516.88810.9890.1850.4561000.7430.766
1.95-1.9916.88810.9480.1540.4471000.620.639
1.99-2.0416.68860.9540.1350.4591000.5420.559
2.04-2.0816.58850.9770.1130.4581000.4490.464
2.08-2.1416.58840.9780.0890.4591000.3530.365
2.14-2.1916.48880.9840.0790.4581000.3140.324
2.19-2.2616.39010.9910.0580.4661000.2290.236
2.26-2.3315.78780.9920.050.4871000.1930.199
2.33-2.4113.98900.9930.0470.5041000.170.176
2.41-2.5116.69150.9960.0370.599.90.1480.153
2.51-2.6317.18870.9980.0290.49899.90.1160.119
2.63-2.7616.79040.9980.0260.5231000.1030.106
2.76-2.9416.48990.9980.0230.5361000.0890.092
2.94-3.1616.19170.9990.0190.5921000.0730.075
3.16-3.4814.19180.9990.0160.6431000.0570.059
3.48-3.9916.29260.9990.0130.6981000.0510.053
3.99-5.0215.99430.9990.0120.7341000.0450.047
5.02-501410300.9990.0120.7499.60.0460.048

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2Q

2r2q


Resolution: 1.85→30.118 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.2222 910 5.04 %
Rwork0.1813 --
obs0.1832 18042 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.07 Å2 / Biso mean: 37.7709 Å2 / Biso min: 17.03 Å2
Refinement stepCycle: final / Resolution: 1.85→30.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 6 63 1238
Biso mean--65.5 38.18 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111212
X-RAY DIFFRACTIONf_angle_d1.1131644
X-RAY DIFFRACTIONf_chiral_restr0.073169
X-RAY DIFFRACTIONf_plane_restr0.008217
X-RAY DIFFRACTIONf_dihedral_angle_d9966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8465-1.96220.26821550.235527812936
1.9622-2.11370.24541650.212627712936
2.1137-2.32630.23281580.201428022960
2.3263-2.66280.27281450.193528603005
2.6628-3.35410.20831340.189428803014
3.3541-30.12150.19831530.156730383191
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)
17.9242-0.0213-0.49895.11586.81289.1013-0.2418-0.1709-0.52090.69130.16420.25520.41050.0880.04640.4599-0.08160.03490.27210.05540.2991-18.910341.695369.4564
26.3176-3.44930.34397.8108-2.73255.021-0.0206-0.92830.30431.0117-0.0041-0.1265-0.2682-0.01720.02260.5864-0.17880.02170.4032-0.06860.2008-23.367656.70979.8035
34.5488-1.6612-1.28325.96673.51124.42850.0554-0.53220.50790.58660.0485-0.6014-0.12320.2592-0.11030.3693-0.144-0.01910.18090.00880.2638-14.80256.950269.1786
42.7139-1.0116-0.90582.07090.7442.84140.0967-0.04260.16430.1946-0.1808-0.0689-0.04780.05590.07270.2633-0.1038-0.0240.12710.01470.1995-18.093156.310862.6985
54.80364.4617-0.03478.18811.03855.46530.3379-0.2716-0.09110.6916-0.2371-0.08010.11410.1066-0.03150.5828-0.2362-0.03770.2805-0.06060.3446-14.357965.462374.2208
66.39972.3160.39198.67212.82916.0925-0.22950.44520.33790.0659-0.0002-0.1555-0.1759-0.03370.26630.5969-0.19150.0510.2570.06810.4195-14.93670.377856.117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 3 )A-5 - 3
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 24 )A4 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 47 )A25 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 117 )A48 - 117
5X-RAY DIFFRACTION5chain 'B' and (resid 1986 through 1993 )B1986 - 1993
6X-RAY DIFFRACTION6chain 'B' and (resid 1994 through 2007 )B1994 - 2007

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