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- PDB-5yir: Crystal Structure of AnkB LIR/GABARAP complex -

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Basic information

Entry
Database: PDB / ID: 5yir
TitleCrystal Structure of AnkB LIR/GABARAP complex
Components
  • Ankyrin-2
  • Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / TBC/RABGAPs / Macroautophagy / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly ...protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / TBC/RABGAPs / Macroautophagy / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly / positive regulation of protein K48-linked ubiquitination / protein localization to organelle / sarcoplasmic reticulum calcium ion transport / positive regulation of potassium ion import across plasma membrane / potassium channel activator activity / A band / regulation of atrial cardiac muscle cell action potential / regulation of Rac protein signal transduction / channel activator activity / phosphorylation-dependent protein binding / atrial cardiac muscle cell action potential / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cytoskeletal anchor activity / atrial septum development / GABA receptor binding / costamere / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / phosphatidylethanolamine binding / response to methylmercury / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / regulation of cardiac muscle cell contraction / M band / protein localization to cell surface / regulation of cardiac muscle contraction by calcium ion signaling / Interaction between L1 and Ankyrins / microtubule associated complex / spectrin binding / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / autophagosome membrane / intercalated disc / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / beta-tubulin binding / COPI-mediated anterograde transport / sperm midpiece / T-tubule / regulation of heart rate / autophagosome / protein localization to plasma membrane / recycling endosome / sarcolemma / GABA-ergic synapse / regulation of protein stability / structural constituent of cytoskeleton / autophagy / microtubule cytoskeleton organization / Z disc / endocytosis / intracellular calcium ion homeostasis / intracellular protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / ATPase binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / microtubule binding / basolateral plasma membrane / microtubule / transmembrane transporter binding / postsynaptic membrane / early endosome / cytoskeleton / lysosome / neuron projection / protein stabilization / apical plasma membrane / Golgi membrane / ubiquitin protein ligase binding / positive regulation of gene expression / protein kinase binding / enzyme binding / Golgi apparatus / mitochondrion / plasma membrane / cytosol
Similarity search - Function
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) ...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
NICKEL (II) ION / Ankyrin-2 / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 ...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.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
D: Gamma-aminobutyric acid receptor-associated protein
A: Gamma-aminobutyric acid receptor-associated protein
B: Gamma-aminobutyric acid receptor-associated protein
C: Ankyrin-2
G: Ankyrin-2
H: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,12316
Polymers51,5366
Non-polymers58710
Water37821
1
D: Gamma-aminobutyric acid receptor-associated protein
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3555
Polymers17,1792
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-28 kcal/mol
Surface area7340 Å2
MethodPISA
2
A: Gamma-aminobutyric acid receptor-associated protein
G: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4136
Polymers17,1792
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-25 kcal/mol
Surface area7200 Å2
MethodPISA
3
B: Gamma-aminobutyric acid receptor-associated protein
H: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3555
Polymers17,1792
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-27 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.637, 84.637, 89.344
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 1987 through 2001 or (resid 2002...
21(chain G and (resid 1987 through 2001 or (resid 2002...
31(chain H and resid 1987 through 2004)
12(chain A and (resid 1 through 65 or (resid 66...
22(chain B and (resid 1 through 23 or (resid 24...
32(chain D and (resid 1 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resid 1987 through 2001 or (resid 2002...C0
211(chain G and (resid 1987 through 2001 or (resid 2002...G0
311(chain H and resid 1987 through 2004)H1987 - 2004
112(chain A and (resid 1 through 65 or (resid 66...A1 - 65
122(chain A and (resid 1 through 65 or (resid 66...A66
132(chain A and (resid 1 through 65 or (resid 66...A1 - 117
142(chain A and (resid 1 through 65 or (resid 66...A1 - 117
152(chain A and (resid 1 through 65 or (resid 66...A1 - 117
162(chain A and (resid 1 through 65 or (resid 66...A1 - 117
172(chain A and (resid 1 through 65 or (resid 66...A1 - 117
182(chain A and (resid 1 through 65 or (resid 66...A1 - 117
212(chain B and (resid 1 through 23 or (resid 24...B1 - 23
222(chain B and (resid 1 through 23 or (resid 24...B24
232(chain B and (resid 1 through 23 or (resid 24...B1 - 117
242(chain B and (resid 1 through 23 or (resid 24...B1 - 117
252(chain B and (resid 1 through 23 or (resid 24...B1 - 117
262(chain B and (resid 1 through 23 or (resid 24...B1 - 117
272(chain B and (resid 1 through 23 or (resid 24...B1 - 117
312(chain D and (resid 1 through 6 or (resid 7...D1 - 6
322(chain D and (resid 1 through 6 or (resid 7...D7
332(chain D and (resid 1 through 6 or (resid 7...D1 - 117
342(chain D and (resid 1 through 6 or (resid 7...D1 - 117
352(chain D and (resid 1 through 6 or (resid 7...D1 - 117
362(chain D and (resid 1 through 6 or (resid 7...D1 - 117

NCS ensembles :
ID
1
2

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein


Mass: 13942.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gabarap / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DCD6
#2: Protein/peptide Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 3236.489 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1588-1614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)

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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: 2.75→50 Å / Num. obs: 18585 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 52.18 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.047 / Rrim(I) all: 0.11 / Χ2: 0.468 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.40.569260.8630.2660.6210.44299.9
2.8-2.855.40.5129290.8630.2430.5670.44999.9
2.85-2.95.40.4579570.8980.2190.5070.443100
2.9-2.965.30.3939300.910.1890.4370.43899.9
2.96-3.035.40.3299240.9490.1580.3660.439100
3.03-3.15.30.2699140.9620.1290.2980.452100
3.1-3.175.10.2319560.9720.1130.2570.45199.8
3.17-3.2650.2029330.9680.1010.2260.431100
3.26-3.364.80.1629180.9810.0810.1810.44899.4
3.36-3.464.30.138880.9830.0690.1480.47197.3
3.46-3.5950.1219270.9870.060.1350.45798.3
3.59-3.735.60.1039550.9920.0480.1140.46599.9
3.73-3.95.60.099170.9940.0420.10.474100
3.9-4.115.50.0819240.9940.0380.090.48100
4.11-4.365.50.079410.9950.0330.0770.497100
4.36-4.75.50.0639400.9960.030.070.539100
4.7-5.175.30.0589120.9960.0280.0640.474100
5.17-5.925.10.0649350.9950.0310.0720.47899.6
5.92-7.464.70.0589250.9950.030.0660.48998.5
7.46-505.70.0489340.9970.0220.0530.53799.9

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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: 1KJT

1kjt


Resolution: 2.75→27.591 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2238 956 5.16 %
Rwork0.1825 --
obs0.1846 18543 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 49.6596 Å2 / Biso min: 22.49 Å2
Refinement stepCycle: final / Resolution: 2.75→27.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 10 21 3344
Biso mean--70.58 46.69 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063399
X-RAY DIFFRACTIONf_angle_d1.1194603
X-RAY DIFFRACTIONf_chiral_restr0.076491
X-RAY DIFFRACTIONf_plane_restr0.006597
X-RAY DIFFRACTIONf_dihedral_angle_d9.4192037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C243X-RAY DIFFRACTION13.03TORSIONAL
12G243X-RAY DIFFRACTION13.03TORSIONAL
13H243X-RAY DIFFRACTION13.03TORSIONAL
21A1695X-RAY DIFFRACTION13.03TORSIONAL
22B1695X-RAY DIFFRACTION13.03TORSIONAL
23D1695X-RAY DIFFRACTION13.03TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.89320.30341360.23552515100
2.8932-3.07420.28091640.22622499100
3.0742-3.31120.24671210.21122530100
3.3112-3.64380.2641370.1849250098
3.6438-4.16950.22841520.16692490100
4.1695-5.24720.16421440.15472516100
5.2472-27.5910.20641020.1811253799

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