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- PDB-5osa: GLIC-GABAAR alpha1 chimera crystallized at pH4.6 -

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Entry
Database: PDB / ID: 5osa
TitleGLIC-GABAAR alpha1 chimera crystallized at pH4.6
ComponentsProton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
KeywordsTRANSPORT PROTEIN / GABAA-receptor ion channel Ion transport Extracellular ligand gated ion channel
Function / homologyNeurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel transmembrane domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Gamma-aminobutyric-acid A receptor, alpha 2 subunit / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / rt:r-mmu-977441: / Neurotransmitter-gated ion-channels signature. ...Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel transmembrane domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Gamma-aminobutyric-acid A receptor, alpha 2 subunit / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / rt:r-mmu-977441: / Neurotransmitter-gated ion-channels signature. / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / regulation of neurotransmitter levels / benzodiazepine receptor activity / inhibitory extracellular ligand-gated ion channel activity / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / regulation of postsynaptic membrane potential / synaptic transmission, GABAergic / inhibitory synapse / neurotransmitter transport / gamma-aminobutyric acid signaling pathway / integral component of postsynaptic specialization membrane / integral component of synaptic vesicle membrane / chloride transport / sodium channel activity / chloride channel activity / chloride channel complex / chloride transmembrane transport / GABA-ergic synapse / dendrite membrane / potassium channel activity / nervous system process / extracellular ligand-gated ion channel activity / ion transmembrane transport / regulation of membrane potential / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / postsynapse / transmembrane signaling receptor activity / chemical synaptic transmission / cell junction / synapse / neuron projection / axon / dendrite / neuronal cell body / integral component of plasma membrane / signal transduction / integral component of membrane / identical protein binding / plasma membrane / Gamma-aminobutyric acid receptor subunit alpha-1 / Gamma-aminobutyric acid receptor subunit alpha-2 / Proton-gated ion channel
Function and homology information
Specimen sourceGloeobacter violaceus (Cyanobacteria)
Mus musculus (house mouse)
Eurypyga helias (sunbittern)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75000236232 Å
AuthorsLaverty, D.C. / Gold, M.G. / Smart, T.G.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.
Authors: Laverty, D. / Thomas, P. / Field, M. / Andersen, O.J. / Gold, M.G. / Biggin, P.C. / Gielen, M. / Smart, T.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2017 / Release: Oct 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 11, 2017Structure modelrepositoryInitial release
1.1Nov 15, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jan 31, 2018Structure modelDatabase referencespdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
B: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
C: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
D: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
E: Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,73833
Polyers193,2215
Non-polymers4,51728
Water63135
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)26670
ΔGint (kcal/M)-188
Surface area (Å2)61500
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)185.017, 133.947, 162.697
Angle α, β, γ (deg.)90.000, 103.535, 90.000
Int Tables number5
Space group name H-MC 1 2 1
Space group name HallC 2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDSelection detailsAuth asym-IDAuth seq-ID
11(chain 'A' and (resid 3 through 48 or resid 50 through 415))A3 - 48
12(chain 'A' and (resid 3 through 48 or resid 50 through 415))A50 - 193
13(chain 'A' and (resid 3 through 48 or resid 50 through 415))A223 - 318
14(chain 'A' and (resid 3 through 48 or resid 50 through 415))A390 - 415
21(chain 'B' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))B3 - 48
22(chain 'B' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))B50 - 193
23(chain 'B' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))B223 - 318
24(chain 'B' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))B390 - 415
31(chain 'C' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))C3 - 48
32(chain 'C' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))C50 - 193
33(chain 'C' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))C223 - 318
34(chain 'C' and (resid 3 through 48 or resid 50 through 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through 415))C390 - 415
41(chain 'D' and (resid 3 through 48 or resid 50 through 415))D3 - 48
42(chain 'D' and (resid 3 through 48 or resid 50 through 415))D50 - 193
43(chain 'D' and (resid 3 through 48 or resid 50 through 415))D223 - 318
44(chain 'D' and (resid 3 through 48 or resid 50 through 415))D390 - 415
51(chain 'E' and (resid 3 through 48 or resid 50 through 415))E3 - 48
52(chain 'E' and (resid 3 through 48 or resid 50 through 415))E50 - 193
53(chain 'E' and (resid 3 through 48 or resid 50 through 415))E223 - 318
54(chain 'E' and (resid 3 through 48 or resid 50 through 415))E390 - 415

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Components

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Protein/peptide , 1 types, 5 molecules ABCDE

#1: Protein/peptide
Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1 / GLIC / Ligand-gated ion channel / LGIC / GABA(A) receptor subunit alpha-2


Mass: 38644.180 Da / Num. of mol.: 5
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (Cyanobacteria), (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eurypyga helias (sunbittern)
Strain: PCC 7421 / Gene: glvI, glr4197, Gabra2, Gabra-2, N326_04548 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7NDN8, UniProt: P26048, UniProt: A0A093IEU4

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Non-polymers , 5 types, 63 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Formula: C2H3O2 / Acetate
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Formula: Cl / Chloride
#4: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 8 / Formula: C12H26 / Dodecane
#5: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 5 / Formula: C31H50O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Formula: H2O / Water

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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: 5.48 Å3/Da / Density % sol: 77.54 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM NaCl, 100 mM sodium acetate pH 4.6, 12 % PEG 6000
pH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→95.28 Å / Num. obs: 100157 / % possible obs: 99.48 % / Redundancy: 3.5 % / Biso Wilson estimate: 60.7400653892 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.068 / Rpim I all: 0.066 / Net I/σ(I): 1.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4988 / CC1/2: 0.868 / Rpim I all: 0.73 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTERdev_2645refinement
PHENIXdev_2645refinement
xia2data processing
PHASERphasing
BUCCANEERmodel building
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFI
Resolution: 2.75000236232→29.9797579828 Å / SU ML: 0.298040544675 / Cross valid method: FREE R-VALUE / σ(F): 1.32870987971 / Phase error: 30.0889651029
RfactorNum. reflection% reflection
Rfree0.22885768459450285.04039938248 %
Rwork0.203369539203--
obs0.204630867049975499.5668143889 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 89.8610594938 Å2
Refinement stepCycle: LAST / Resolution: 2.75000236232→29.9797579828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245703103512802
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0051118776811213084
f_angle_d0.81266883371617898
f_chiral_restr0.04903478657012100
f_plane_restr0.004344739951812225
f_dihedral_angle_d9.677538118617687
Refine LS shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.78120.3911199440351920.344497592225316799.1733097136
2.7812-2.81390.3745686613861620.320978947516312199.3343419062
2.8139-2.84820.3350341483711690.313094708582316599.0787518574
2.8482-2.88420.3133978093481770.302996388977305299.109883364
2.8842-2.92220.327144475291780.304513495848316499.3755575379
2.9222-2.96220.3297072326251670.279857389274313299.3076459964
2.9622-3.00440.3328650992031750.286458082562314599.520383693
3.0044-3.04920.3229422919721700.284526251864309599.8470948012
3.0492-3.09680.2727819012731620.260049674552320599.8813408484
3.0968-3.14760.3060488391221760.248742512556308799.5727799817
3.1476-3.20180.3036176502681710.240293882027317299.553305539
3.2018-3.25990.262666072551680.231365900397317399.5530393325
3.2599-3.32260.3014975866341600.233498405077310099.3296770262
3.3226-3.39030.2515973311751970.234712554254311699.2510485321
3.3903-3.46390.267722650521760.235565324549316699.3755575379
3.4639-3.54430.2715999051431710.234482682105313399.7885835095
3.5443-3.63280.2585820195251770.2114797536314099.3708807669
3.6328-3.73090.2200646369231570.196883437229313999.7578692494
3.7309-3.84050.2006362474221610.187447256946318199.8804542738
3.8405-3.96410.2033697356061520.1908697054783194100
3.9641-4.10550.2277818826681610.178624441988314899.9395952884
4.1055-4.26940.1992639044671840.164057503215316099.880525687
4.2694-4.46310.1785291938541440.162212269909320299.8805970149
4.4631-4.69760.1624208676871540.139997762197318499.910206525
4.6976-4.99070.1750058345121710.150522803745317599.6129800536
4.9907-5.3740.2036044752061510.168192191704317199.699879952
5.374-5.9110.2018318445081520.1844210954663199100
5.911-6.75780.2158708084191500.201539248597322899.7637330183
6.7578-8.48210.1851950240781670.1833214740143205100
8.4821-29.98150.2090291815021760.218633836252320798.3716196569
Refine TLSMethod: refined / Origin x: 47.5064551016 Å / Origin y: 1.41407561932 Å / Origin z: 26.7417564881 Å
111213212223313233
T0.474402783567 Å20.0675798665437 Å20.0305613785697 Å2-0.450043386015 Å2-0.0216819510558 Å2--0.528687976533 Å2
L0.760952887066 deg.20.0653086152909 deg.20.580180143994 deg.2-0.524685589918 deg.20.0519566670012 deg.2--1.4267637436 deg.2
S0.0320911156957 Å deg.0.0183470764553 Å deg.-0.00898994364437 Å deg.-0.116202281694 Å deg.-0.0390207097291 Å deg.0.0808766516708 Å deg.-0.0456070729424 Å deg.0.00830701882021 Å deg.-8.03473689378E-5 Å deg.
Refine TLS groupSelection details: all

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