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- PDB-7cdb: Structure of GABARAPL1 in complex with GABA(A) receptor gamma 2 -

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Basic information

Entry
Database: PDB / ID: 7cdb
TitleStructure of GABARAPL1 in complex with GABA(A) receptor gamma 2
Components
  • Gamma-aminobutyric acid receptor subunit gamma-2
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


substrate localization to autophagosome / GABA receptor activation / Macroautophagy / glycophagy / inhibitory synapse / GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly ...substrate localization to autophagosome / GABA receptor activation / Macroautophagy / glycophagy / inhibitory synapse / GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / autophagy of mitochondrion / Tat protein binding / GABA receptor binding / cellular response to nitrogen starvation / neurotransmitter receptor activity / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / adult behavior / chloride channel activity / autophagosome membrane / chloride channel complex / autophagosome assembly / GABA-ergic synapse / autophagosome / regulation of postsynaptic membrane potential / protein-membrane adaptor activity / chloride transmembrane transport / dendrite membrane / dendrite cytoplasm / cytoskeletal protein binding / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / macroautophagy / cytoplasmic vesicle membrane / cell body / chemical synaptic transmission / postsynapse / microtubule / neuron projection / axon / glutamatergic synapse / synapse / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsLi, J. / Ye, J. / Zhu, R. / Kong, C. / Zhang, M. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670734 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of GABARAP-mediated GABA A receptor trafficking and functions on GABAergic synaptic transmission.
Authors: Ye, J. / Zou, G. / Zhu, R. / Kong, C. / Miao, C. / Zhang, M. / Li, J. / Xiong, W. / Wang, C.
History
DepositionJun 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Gamma-aminobutyric acid receptor subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8136
Polymers31,3693
Non-polymers4433
Water1,51384
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8943
Polymers14,6431
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Gamma-aminobutyric acid receptor subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9193
Polymers16,7272
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.379, 89.379, 115.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-319-

HOH

31A-324-

HOH

41A-347-

HOH

51A-348-

HOH

61B-311-

HOH

71B-334-

HOH

DetailsIn the crystal, the binding pocket of chain A for GABA(A) receptor is blocked by the ligand CIT. This prevents chain A from forming a heterodimer with another molecular of GABA(A) receptor.

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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.: 2
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 Gamma-aminobutyric acid receptor subunit gamma-2 / GABA(A) receptor subunit gamma-2


Mass: 2084.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gabrg2 / Production host: Escherichia coli (E. coli) / References: UniProt: P22723
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH 5.6, and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 19730 / % possible obs: 96.4 % / Redundancy: 14.3 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.059 / Rrim(I) all: 0.228 / Χ2: 1.332 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9813.90.9619670.7750.2650.9990.97398.3
1.98-2.0214.10.8449790.7790.230.8770.9898.2
2.02-2.06140.7429830.8460.2040.7711.00298.3
2.06-2.114.20.6449750.8670.1750.6691.00598.1
2.1-2.1514.20.639880.8840.1720.6551.00797.9
2.15-2.214.30.5449680.9030.1480.5651.02597.7
2.2-2.2514.20.4749830.9230.1290.4921.05197.6
2.25-2.3114.40.4269840.9390.1150.4421.06297.3
2.31-2.3814.40.4169630.9460.1130.4321.06597.4
2.38-2.4614.60.3839800.9430.1030.3971.08196.9
2.46-2.5414.60.3079870.9670.0820.3191.0997.1
2.54-2.6514.60.2929840.9660.0780.3031.10996.7
2.65-2.7714.80.2399770.9780.0640.2481.14796.5
2.77-2.9114.70.2249830.9840.060.2331.21296.3
2.91-3.114.60.199920.9850.050.1971.46796.1
3.1-3.3314.60.1519840.9930.040.1571.95995.5
3.33-3.6714.30.1329820.9950.0350.1372.23895.2
3.67-4.214.20.1119960.9950.0290.1152.44194.3
4.2-5.2914.10.07910060.9970.0210.0821.91293.3
5.29-5013.80.07610690.9980.020.0791.74190.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2Q

2r2q


Resolution: 1.949→36.681 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 982 4.98 %
Rwork0.1974 18747 -
obs0.1991 19729 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.02 Å2 / Biso mean: 19.462 Å2 / Biso min: 3.75 Å2
Refinement stepCycle: final / Resolution: 1.949→36.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 30 84 2225
Biso mean--31.73 16.86 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082223
X-RAY DIFFRACTIONf_angle_d0.9673018
X-RAY DIFFRACTIONf_chiral_restr0.065304
X-RAY DIFFRACTIONf_plane_restr0.007400
X-RAY DIFFRACTIONf_dihedral_angle_d20.2631339
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9492-2.05190.25921580.2162264298
2.0519-2.18050.28991280.215265498
2.1805-2.34880.26641450.2097266698
2.3488-2.58510.23571230.2182265297
2.5851-2.95910.26751360.2147267397
2.9591-3.72750.22971330.1891269696
3.7275-36.6810.1781590.1689276493
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)
11.124-0.57250.6721.70970.58461.0094-0.1589-0.3293-0.24950.0609-0.0026-0.1438-0.03750.15190.12750.0572-0.0019-0.01350.1040.04710.111120.65161.333912.6358
20.1261-0.3834-0.45581.52881.64571.83230.10920.21170.1733-0.36540.0269-0.2471-0.58750.1063-0.18960.1882-0.02050.05710.23780.05660.1611127.438867.765-1.7786
30.8957-0.0362-0.13871.0336-0.09281.6213-0.08440.1175-0.1408-0.1591-0.0631-0.24220.17070.22260.09790.09960.00540.03180.11690.00250.1087119.758551.4244-0.0196
41.00830.28190.11871.07470.41310.8677-0.00220.0403-0.1038-0.1342-0.0627-0.05270.10930.1098-0.00580.06340.00720.00180.0582-0.00090.062113.316954.88444.0834
52.8121-1.9835-0.83593.51931.86951.0211-0.0495-0.08730.13340.210.11250.1049-0.1187-0.2005-0.02810.10670.02260.06530.1104-0.02580.1177129.798332.8188-3.1164
60.0329-0.02470.11330.4417-0.15290.40550.00880.0940.1184-0.1174-0.05730.0699-0.1102-0.0162-0.15410.26470.1448-0.0590.2390.09840.3249125.600343.4733-16.287
71.59010.72450.82081.53480.56282.98490.083-0.04160.2920.0293-0.1510.0206-0.1157-0.0250.03610.11390.03920.05280.12370.02240.1447137.697341.5454-5.9063
81.1645-0.9672-0.2741.34310.18360.91030.08690.00540.29210.01150.00910.0169-0.28180.01430.06910.1738-0.01710.0550.04930.00120.1494145.2543.0927-10.4009
94.8780.53671.72283.79131.1314.99230.0859-0.32260.44240.30720.0432-0.4411-0.46140.3150.06960.1546-0.02020.02230.1196-0.0210.1689149.954336.0046-0.8265
102.588-0.18540.42631.3933-0.13170.20830.04980.0493-0.0068-0.08-0.04550.0352-0.0945-0.1002-0.01270.07340.03440.00710.07310.00910.0715138.86832.8188-11.2679
114.80170.13431.38311.9863-0.38933.3424-0.00920.09710.4787-0.01790.02220.1341-0.6139-0.22270.00260.35780.0180.13990.15390.01450.4284136.062951.6428-11.3484
122.35521.67980.24336.5539-3.3032.2816-0.06670.18820.13210.06030.22770.51960.0096-0.1203-0.20910.6967-0.32190.28530.5555-0.15650.6392152.708849.2218-11.1297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 10 )A-4 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 24 )A11 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 67 )A25 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 117 )A68 - 117
5X-RAY DIFFRACTION5chain 'B' and (resid -4 through 10 )B-4 - 10
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 24 )B11 - 24
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 47 )B25 - 47
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 68 )B48 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 79 )B69 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 117 )B80 - 117
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 57 )C49 - 57
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 63 )C58 - 63

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