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- PDB-6cdu: Crystal structure of a chimeric human alpha1GABAA receptor in com... -

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Basic information

Entry
Database: PDB / ID: 6cdu
TitleCrystal structure of a chimeric human alpha1GABAA receptor in complex with alphaxalone
Componentschimeric alpha1GABAA receptor
KeywordsPROTEIN TRANSPORT / GABAA receptor / anesthetics / alphaxalone / neurosteroids
Function / homology
Function and homology information


GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / GABA-gated chloride ion channel activity / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / Signaling by ERBB4 ...GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / GABA-gated chloride ion channel activity / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / Signaling by ERBB4 / extracellular ligand-gated monoatomic ion channel activity / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / chloride transmembrane transport / dendrite membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / transmembrane signaling receptor activity / postsynaptic membrane / postsynapse / neuron projection / synapse / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 ...: / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
(3a,5a)-3-Hydroxypregnane-11,20-dione / Gamma-aminobutyric-acid receptor subunit beta-1 / Gamma-aminobutyric acid receptor subunit alpha-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsChen, Q. / Arjunan, P. / Cohen, A.E. / Xu, Y. / Tang, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM056257 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of neurosteroid anesthetic action on GABAAreceptors.
Authors: Chen, Q. / Wells, M.M. / Arjunan, P. / Tillman, T.S. / Cohen, A.E. / Xu, Y. / Tang, P.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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 / _entity.formula_weight
Revision 1.3Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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 / _entity.formula_weight
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: chimeric alpha1GABAA receptor
B: chimeric alpha1GABAA receptor
C: chimeric alpha1GABAA receptor
D: chimeric alpha1GABAA receptor
E: chimeric alpha1GABAA receptor
F: chimeric alpha1GABAA receptor
G: chimeric alpha1GABAA receptor
H: chimeric alpha1GABAA receptor
I: chimeric alpha1GABAA receptor
J: chimeric alpha1GABAA receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,57820
Polymers372,25410
Non-polymers3,32510
Water0
1
A: chimeric alpha1GABAA receptor
B: chimeric alpha1GABAA receptor
C: chimeric alpha1GABAA receptor
D: chimeric alpha1GABAA receptor
E: chimeric alpha1GABAA receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,78910
Polymers186,1275
Non-polymers1,6625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-130 kcal/mol
Surface area64060 Å2
MethodPISA
2
F: chimeric alpha1GABAA receptor
G: chimeric alpha1GABAA receptor
H: chimeric alpha1GABAA receptor
I: chimeric alpha1GABAA receptor
J: chimeric alpha1GABAA receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,78910
Polymers186,1275
Non-polymers1,6625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-134 kcal/mol
Surface area63610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.202, 263.529, 109.160
Angle α, β, γ (deg.)90.00, 110.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
chimeric alpha1GABAA receptor / GABA(A) receptor subunit alpha-1


Mass: 37225.359 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: 3937 / Gene: Dda3937_00520, GABRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4, UniProt: P14867
#2: Chemical
ChemComp-EY4 / (3a,5a)-3-Hydroxypregnane-11,20-dione / alphaxalone / Alfaxalone


Mass: 332.477 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H32O3

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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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: PEG400, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, NaSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.45→39.88 Å / Num. obs: 73186 / % possible obs: 97.8 % / Redundancy: 14.4 % / Biso Wilson estimate: 119 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.042 / Χ2: 0.98 / Net I/σ(I): 13.2
Reflection shellResolution: 3.45→3.52 Å / Redundancy: 14.4 % / Rmerge(I) obs: 3.252 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4610 / CC1/2: 0.488 / Rpim(I) all: 0.877 / Χ2: 0.97 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z90, apo structure

4z90


Resolution: 3.45→39.879 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.95
RfactorNum. reflection% reflection
Rfree0.2861 3580 4.9 %
Rwork0.2267 --
obs0.2296 73029 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.45→39.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25690 0 240 0 25930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326640
X-RAY DIFFRACTIONf_angle_d0.66136360
X-RAY DIFFRACTIONf_dihedral_angle_d2.42415500
X-RAY DIFFRACTIONf_chiral_restr0.0474100
X-RAY DIFFRACTIONf_plane_restr0.0044550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.49540.42081640.36462647X-RAY DIFFRACTION97
3.4954-3.54320.42341340.34642661X-RAY DIFFRACTION99
3.5432-3.59380.36381310.31482732X-RAY DIFFRACTION99
3.5938-3.64740.37651110.29712722X-RAY DIFFRACTION99
3.6474-3.70440.34091400.29562693X-RAY DIFFRACTION99
3.7044-3.76510.37631450.29682701X-RAY DIFFRACTION99
3.7651-3.82990.35571140.30162688X-RAY DIFFRACTION98
3.8299-3.89950.36311500.28472677X-RAY DIFFRACTION98
3.8995-3.97450.39321470.28292644X-RAY DIFFRACTION97
3.9745-4.05550.34091240.27912472X-RAY DIFFRACTION91
4.0555-4.14360.30131360.24142369X-RAY DIFFRACTION88
4.1436-4.23990.33721240.22942703X-RAY DIFFRACTION98
4.2399-4.34580.24881260.21972743X-RAY DIFFRACTION100
4.3458-4.46310.2491370.20792736X-RAY DIFFRACTION100
4.4631-4.59430.24421480.19142720X-RAY DIFFRACTION100
4.5943-4.74240.23991530.16762722X-RAY DIFFRACTION99
4.7424-4.91160.22551430.16492709X-RAY DIFFRACTION99
4.9116-5.10780.21621400.16192687X-RAY DIFFRACTION99
5.1078-5.33980.23251390.1862698X-RAY DIFFRACTION99
5.3398-5.62060.26221190.19492752X-RAY DIFFRACTION99
5.6206-5.97170.26671410.21422687X-RAY DIFFRACTION98
5.9717-6.4310.30091370.23392728X-RAY DIFFRACTION99
6.431-7.07490.29261480.23382655X-RAY DIFFRACTION98
7.0749-8.09120.28461190.21672489X-RAY DIFFRACTION91
8.0912-10.16610.21891570.18612661X-RAY DIFFRACTION97
10.1661-39.88140.32621530.26122753X-RAY DIFFRACTION99
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)
10.35420.53130.95241.40351.60433.7457-0.04480.33310.5389-0.82410.13710.3558-0.58050.04510.00021.41350.1404-0.25571.25710.07921.2281-31.763846.2789-16.3487
24.6061-0.44821.50912.90460.27830.49130.1953-0.09320.89890.24210.1408-0.1739-0.5937-0.2640.00041.30290.18950.11781.2077-0.18781.2702-33.72655.579433.2431
33.0831-0.74870.23963.64370.56993.20530.23050.2795-0.2835-0.7489-0.2630.4390.0037-0.24060.00051.0341-0.1049-0.30731.2434-0.15431.0849-34.646720.1867-11.5683
42.3093-1.694-0.2825-0.10992.04240.7965-0.2898-1.0233-0.20940.25010.03370.40471.1580.3406-0.00181.3327-0.06670.23451.3887-0.02611.1249-39.400234.871836.4998
52.70940.8924-1.27483.1748-1.27484.7147-0.05330.1236-0.30530.0350.02920.11720.0116-0.36390.00011.3920.04330.11190.9116-0.08560.9568-10.422310.2292-5.8731
61.1146-0.45740.1670.84170.71761.3196-0.0555-0.4614-0.56240.9730.00620.3671-0.051-0.46790.00191.86550.06890.4171.1838-0.01810.8925-21.192723.8241.5642
73.1952-0.40670.02635.9110.16553.54360.09340.172-0.1085-0.55680.075-0.87440.17420.135401.12490.00090.15480.8992-0.06691.03597.42430.0461-7.1125
82.4040.67820.17351.17680.18010.9132-0.0245-0.57850.0821-0.0148-0.1012-0.5520.02-0.40480.00061.06140.190.03331.2868-0.07490.7249-4.368137.638141.3227
92.95310.1590.02530.13620.25055.4220.13250.2090.702-0.29850.0532-0.0061-0.24220.078301.53690.1512-0.01360.92340.07250.9963-5.750352.3182-13.5588
102.3770.15340.59361.6086-1.21611.09220.3292-0.26770.87880.5461-0.35620.1443-0.5307-0.6166-0.00031.98230.08420.29671.138-0.28751.323-12.17757.205536.1623
116.6883-2.10120.71294.52350.11283.3419-0.30840.1389-0.6496-0.64610.28090.57980.45430.14950.0011.2204-0.1644-0.13270.943-0.02251.3464-6.4702-55.76928.0382
120.20250.85920.57612.0206-0.09740.6823-0.7358-0.40061.84560.0725-0.0133-2.31061.2048-0.1994-0.19130.57410.2953-0.6971.4978-0.26322.322340.8508-41.238817.9044
133.6183-0.74192.04580.58352.05681.9221-0.30850.27570.3629-0.5093-0.1597-0.12010.34030.1259-0.0011.4494-0.22510.09931.07760.11551.1838-8.9929-35.534-9.0813
141.0144-0.86690.74110.62070.13642.73810.4716-0.89160.6549-0.2985-0.31940.05210.10350.3933-0.00070.8635-0.09550.04671.2057-0.07851.614639.6075-26.8011.7631
155.0074-0.66830.15982.34540.84114.8963-0.2211-0.1706-0.19650.1899-0.02450.55-0.2924-0.493800.9666-0.02820.11680.8119-0.04451.2293-15.7084-14.03745.2353
161.0446-1.2535-0.12781.6932-1.0461.5499-0.2557-0.3011-0.1481-0.53190.2078-0.8206-0.74140.3803-0.00091.1065-0.2338-0.1481.4164-0.1731.873634.0789-7.617610.3883
175.09642.41650.02680.9422-1.7267-0.0059-0.6206-0.45420.43730.14890.53930.0941-0.27210.0764-0.00040.944-0.03660.02761.3257-0.19860.9643-17.3702-20.896131.1142
181.03951.9661-0.85781.5887-0.3842-0.10640.6184-0.31-0.49881.6205-0.1029-0.86140.2092-0.03350.00240.9706-0.0824-0.31021.3523-0.20221.749332.0277-10.454532.1348
193.37990.7128-0.16413.35920.48712.8389-0.2295-0.49150.12611.35-0.20010.9590.3688-0.1365-0.00141.2555-0.07140.2831.13240.13371.1055-11.8378-46.87532.6308
200.61670.3961-1.027-0.34450.57081.8246-0.0197-0.33691.19590.18250.26320.32770.81611.0350.00061.16080.1433-0.35981.6472-0.1751.801436.1249-31.190936.8343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 199)
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 416)
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 199)
4X-RAY DIFFRACTION4chain 'B' and (resid 222 through 416)
5X-RAY DIFFRACTION5chain 'C' and (resid 10 through 199)
6X-RAY DIFFRACTION6chain 'C' and (resid 222 through 416)
7X-RAY DIFFRACTION7chain 'D' and (resid 10 through 199)
8X-RAY DIFFRACTION8chain 'D' and (resid 222 through 416)
9X-RAY DIFFRACTION9chain 'E' and (resid 10 through 199)
10X-RAY DIFFRACTION10chain 'E' and (resid 222 through 416)
11X-RAY DIFFRACTION11chain 'F' and (resid 10 through 199)
12X-RAY DIFFRACTION12chain 'F' and (resid 222 through 416)
13X-RAY DIFFRACTION13chain 'G' and (resid 10 through 199)
14X-RAY DIFFRACTION14chain 'G' and (resid 222 through 416)
15X-RAY DIFFRACTION15chain 'H' and (resid 10 through 199)
16X-RAY DIFFRACTION16chain 'H' and (resid 222 through 416)
17X-RAY DIFFRACTION17chain 'I' and (resid 10 through 199)
18X-RAY DIFFRACTION18chain 'I' and (resid 222 through 416)
19X-RAY DIFFRACTION19chain 'J' and (resid 10 through 199)
20X-RAY DIFFRACTION20chain 'J' and (resid 222 through 416)

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