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- PDB-6a9x: Crystal Structure of AnkG/GABARAP Complex -

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Basic information

Entry
Database: PDB / ID: 6a9x
TitleCrystal Structure of AnkG/GABARAP Complex
Components
  • Ankyrin-3
  • Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN BINDING / STRUCTURAL PROTEIN / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / membrane assembly / TBC/RABGAPs / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels ...positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / regulation of protein targeting / maintenance of protein location in plasma membrane / membrane assembly / TBC/RABGAPs / Macroautophagy / protein localization to axon / clustering of voltage-gated sodium channels / positive regulation of sodium ion transmembrane transporter activity / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / spectrin-associated cytoskeleton / magnesium ion homeostasis / positive regulation of protein K48-linked ubiquitination / positive regulation of membrane potential / negative regulation of delayed rectifier potassium channel activity / plasma membrane organization / phosphorylation-dependent protein binding / positive regulation of homotypic cell-cell adhesion / positive regulation of cation channel activity / maintenance of protein location in cell / regulation of Rac protein signal transduction / axon initial segment / GABA receptor binding / paranode region of axon / positive regulation of sodium ion transport / Golgi to plasma membrane protein transport / negative regulation of endocytosis / node of Ranvier / costamere / cellular response to magnesium ion / phosphatidylethanolamine binding / regulation of modification of postsynaptic structure / anterograde axonal transport / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / spectrin binding / neuromuscular junction development / axon development / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / mitotic cytokinesis / intercalated disc / neuronal action potential / response to immobilization stress / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome / lateral plasma membrane / positive regulation of protein targeting to membrane / smooth endoplasmic reticulum / GABA-ergic synapse / axon cytoplasm / sperm midpiece / T-tubule / cytoskeletal protein binding / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / axon guidance / protein localization to plasma membrane / synapse organization / establishment of protein localization / neuromuscular junction / structural constituent of cytoskeleton / sarcolemma / Z disc / microtubule cytoskeleton organization / positive regulation of non-canonical NF-kappaB signal transduction / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / protein-macromolecule adaptor activity / cell body / cytoplasmic vesicle / microtubule binding / basolateral plasma membrane / postsynaptic membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / postsynapse / microtubule / lysosome / cytoskeleton / neuron projection / cadherin binding / Golgi membrane / axon / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm
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 / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Death-like domain superfamily / Ankyrin repeat / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsWang, C. / Li, J. / Chen, K. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants CouncilAoE-M09-12 Hong Kong
CitationJournal: Mol. Psychiatry / Year: 2018
Title: Ankyrin-G regulates forebrain connectivity and network synchronization via interaction with GABARAP.
Authors: Nelson, A.D. / Caballero-Floran, R.N. / Rodriguez Diaz, J.C. / Hull, J.M. / Yuan, Y. / Li, J. / Chen, K. / Walder, K.K. / Lopez-Santiago, L.F. / Bennett, V. / McInnis, M.G. / Isom, L.L. / ...Authors: Nelson, A.D. / Caballero-Floran, R.N. / Rodriguez Diaz, J.C. / Hull, J.M. / Yuan, Y. / Li, J. / Chen, K. / Walder, K.K. / Lopez-Santiago, L.F. / Bennett, V. / McInnis, M.G. / Isom, L.L. / Wang, C. / Zhang, M. / Jones, K.S. / Jenkins, P.M.
History
DepositionJul 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
D: Gamma-aminobutyric acid receptor-associated protein
A: Ankyrin-3


Theoretical massNumber of molelcules
Total (without water)16,6362
Polymers16,6362
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-11 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.991, 96.991, 96.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 13942.047 Da / Num. of mol.: 1
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-3 / AnkG / ANK-3 / Ankyrin-G


Mass: 2693.770 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 7843 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 26.93 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Χ2: 0.993 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.2-2.24203670.7920.3350.976100
2.24-2.2820.64000.820.3020.978100
2.28-2.3220.54030.8880.2290.98100
2.32-2.3720.43790.8990.1951.0291000.860.882
2.37-2.4220.53700.9250.170.981000.7550.774
2.42-2.4820.13840.9370.1581.0541000.6950.713
2.48-2.5420.44010.9630.1191.0211000.5270.54
2.54-2.61203930.9790.0930.9851000.4060.417
2.61-2.6919.93840.9850.0741.0011000.3230.331
2.69-2.7718.53930.990.061.0111000.2530.26
2.77-2.8717.63820.9930.0471.0341000.1950.201
2.87-2.99213990.9970.0321.0071000.1450.148
2.99-3.1220.83860.9980.0230.9911000.1030.106
3.12-3.2920.43840.9980.0180.971000.080.082
3.29-3.49204010.9980.0150.9751000.0660.068
3.49-3.7619.43910.9990.0140.9541000.0580.06
3.76-4.1417.23960.9990.0141.0151000.0550.057
4.14-4.74193990.9980.0131.02199.50.0540.055
4.74-5.9719.34110.9990.0120.9131000.0520.054
5.97-5017.54200.9980.0140.96798.80.0580.06

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KJT

1kjt


Resolution: 2.202→30.671 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2489 349 4.51 %
Rwork0.2027 --
obs0.2048 7745 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.03 Å2 / Biso mean: 34.1556 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 2.202→30.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 0 15 1102
Biso mean---31.04 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061116
X-RAY DIFFRACTIONf_angle_d0.9331511
X-RAY DIFFRACTIONf_chiral_restr0.037160
X-RAY DIFFRACTIONf_plane_restr0.003196
X-RAY DIFFRACTIONf_dihedral_angle_d15.336404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2021-2.77410.30841740.25573611378598
2.7741-30.67420.22471750.181937853960100
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)
14.2016-1.6756-1.11983.28450.34641.52570.0483-0.231-0.4587-0.2137-0.2115-0.17480.39820.14360.08260.3638-0.05290.0670.18180.10280.43344.651320.4539114.9783
21.6163-0.749-0.27360.81070.77440.9504-0.0151-0.166-0.2961-0.3714-0.1871-0.53470.09980.1680.15140.19090.01150.08140.17480.07230.24349.405632.114112.4756
34.92271.4305-2.7961.5659-1.93992.6956-0.19990.09370.2802-0.35710.35820.220.2213-0.202-0.11780.2188-0.0690.00030.28440.01250.2413-4.769930.2998115.4047
44.96880.4837-0.34821.47441.00831.97090.0524-0.20590.6487-0.18510.04670.2749-0.0125-0.3213-0.05980.14450.0041-0.0520.3740.08240.3391-9.095737.0099116.8232
50.05090.15240.12560.45660.37660.3108-0.0660.01570.0695-0.10550.01010.0760.0768-0.1585-0.06140.1574-0.0823-0.02120.45480.09610.154-14.266929.9266120.4971
61.58870.3999-0.03360.9478-0.08230.33720.0607-0.43550.06050.0985-0.0382-0.0641-0.02730.119-0.01760.2528-0.09630.01640.9376-0.11990.2677-1.063733.9452127.7662
71.20760.1999-0.66020.1525-0.15840.3810.1209-0.23480.04460.0516-0.1077-0.0815-0.0590.1233-0.11720.1628-0.06830.04390.42350.10590.2191.717529.7597122.507
80.16910.03380.08870.03870.03350.0543-0.17510.19670.0459-0.20250.0127-0.102-0.02220.05550.12050.49070.04250.13030.33860.1010.33940.963435.4044106.2087
92.0047-1.6346-0.47172.01381.34378.49530.31120.03550.5990.09910.32440.3592-0.3895-0.2693-0.62510.40740.08620.03440.28650.10440.5608-8.661246.2858112.7272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 10 )D1 - 10
2X-RAY DIFFRACTION2chain 'D' and (resid 11 through 35 )D11 - 35
3X-RAY DIFFRACTION3chain 'D' and (resid 36 through 56 )D36 - 56
4X-RAY DIFFRACTION4chain 'D' and (resid 57 through 68 )D57 - 68
5X-RAY DIFFRACTION5chain 'D' and (resid 69 through 79 )D69 - 79
6X-RAY DIFFRACTION6chain 'D' and (resid 80 through 90 )D80 - 90
7X-RAY DIFFRACTION7chain 'D' and (resid 91 through 117 )D91 - 117
8X-RAY DIFFRACTION8chain 'A' and (resid 1987 through 1993 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1994 through 2004 )A0

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