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- PDB-3uq4: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 3uq4
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) mutant F247L (F16L)
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / membrane protein / liganded-gated ion channel
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGonzalez-Gutierrez, G. / Lukk, T. / Agarwal, V. / Papke, D. / Nair, S.K. / Grosman, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals.
Authors: Gonzalez-Gutierrez, G. / Lukk, T. / Agarwal, V. / Papke, D. / Nair, S.K. / Grosman, C.
History
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,93712
Polymers369,89110
Non-polymers462
Water00
1
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,9696
Polymers184,9465
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24760 Å2
ΔGint-139 kcal/mol
Surface area66410 Å2
MethodPISA
2
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,9696
Polymers184,9465
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24740 Å2
ΔGint-137 kcal/mol
Surface area66450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.350, 266.940, 110.840
Angle α, β, γ (deg.)90.000, 109.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31D
41E
51H
61A
71F
81G
91I
101J

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLNGLNchain 'B' and (resseq 11:287 or resseq 289:316 )BB11 - 28713 - 289
12ASNASNVALVALchain 'B' and (resseq 11:287 or resseq 289:316 )BB289 - 316291 - 318
21PROPROGLNGLNchain 'C' and (resseq 11:287 or resseq 289:316 )CC11 - 28713 - 289
22ASNASNVALVALchain 'C' and (resseq 11:287 or resseq 289:316 )CC289 - 316291 - 318
31PROPROGLNGLNchain 'D' and (resseq 11:287 or resseq 289:316 )DD11 - 28713 - 289
32ASNASNVALVALchain 'D' and (resseq 11:287 or resseq 289:316 )DD289 - 316291 - 318
41PROPROGLNGLNchain 'E' and (resseq 11:287 or resseq 289:316 )EE11 - 28713 - 289
42ASNASNVALVALchain 'E' and (resseq 11:287 or resseq 289:316 )EE289 - 316291 - 318
51PROPROGLNGLNchain 'H' and (resseq 11:287 or resseq 289:316 )HH11 - 28713 - 289
52ASNASNVALVALchain 'H' and (resseq 11:287 or resseq 289:316 )HH289 - 316291 - 318
61PROPROGLNGLNchain 'A' and (resseq 11:287 or resseq 289:316 )AA11 - 28713 - 289
62ASNASNVALVALchain 'A' and (resseq 11:287 or resseq 289:316 )AA289 - 316291 - 318
71PROPROGLNGLNchain 'F' and (resseq 11:287 or resseq 289:316 )FF11 - 28713 - 289
72ASNASNVALVALchain 'F' and (resseq 11:287 or resseq 289:316 )FF289 - 316291 - 318
81PROPROGLNGLNchain 'G' and (resseq 11:287 or resseq 289:316 )GG11 - 28713 - 289
82ASNASNVALVALchain 'G' and (resseq 11:287 or resseq 289:316 )GG289 - 316291 - 318
91PROPROGLNGLNchain 'I' and (resseq 11:287 or resseq 289:316 )II11 - 28713 - 289
92ASNASNVALVALchain 'I' and (resseq 11:287 or resseq 289:316 )II289 - 316291 - 318
101PROPROGLNGLNchain 'J' and (resseq 11:287 or resseq 289:316 )JJ11 - 28713 - 289
102ASNASNVALVALchain 'J' and (resseq 11:287 or resseq 289:316 )JJ289 - 316291 - 318

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Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1 / ELIC


Mass: 36989.113 Da / Num. of mol.: 10 / Mutation: F246L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 3.97 Å3/Da / Density % sol: 69.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-12% PEG4000, 200 mM ammonium sulfate, 50 mM N-(2-acetamido)iminodiacetic acid (ADA), pH 6.5-6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.5→19.93 Å / Num. obs: 71891 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 78.497 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.5-3.590.7073.3945083526199.3
3.59-3.690.5564.3545576530499.6
3.69-3.80.4824.9644252514099.5
3.8-3.910.3496.6739949465499.4
3.91-4.040.2818.241476482699.9
4.04-4.180.22710.0339121454399.8
4.18-4.340.17812.6338653449999.8
4.34-4.520.12716.6437578436899.9
4.52-4.720.10819.2635114408599.7
4.72-4.950.10220.6333791392799.8
4.95-5.220.09621.532586379399.9
5.22-5.530.09721.4929704346399.7
5.53-5.920.08723.3529181339199.7
5.92-6.390.0922.8826288305799.9
6.39-70.0825.424605287499.6
7-7.830.05533.8222115258599.8
7.83-9.040.03745.3519215226599.7
9.04-11.070.0357.516216194299.4
11.07-15.650.02960.9112143148998.9
15.650.03359.88296942550.7

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Processing

Software
NameVersionClassificationNB
PHENIXdev_897refinement
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.5→19.93 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 1.99 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3595 5 %
Rwork0.2149 --
obs0.2161 71871 99.79 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.48 Å2 / ksol: 0.262 e/Å3
Displacement parametersBiso max: 234.33 Å2 / Biso mean: 102.5078 Å2 / Biso min: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25020 0 2 0 25022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01525690
X-RAY DIFFRACTIONf_angle_d1.74735020
X-RAY DIFFRACTIONf_chiral_restr0.1083910
X-RAY DIFFRACTIONf_plane_restr0.014460
X-RAY DIFFRACTIONf_dihedral_angle_d19.9559230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2489X-RAY DIFFRACTIONPOSITIONAL0.078
12C2489X-RAY DIFFRACTIONPOSITIONAL0.078
13D2489X-RAY DIFFRACTIONPOSITIONAL0.076
14E2489X-RAY DIFFRACTIONPOSITIONAL0.076
15H2489X-RAY DIFFRACTIONPOSITIONAL0.089
16A2489X-RAY DIFFRACTIONPOSITIONAL0.068
17F2489X-RAY DIFFRACTIONPOSITIONAL0.091
18G2489X-RAY DIFFRACTIONPOSITIONAL0.072
19I2489X-RAY DIFFRACTIONPOSITIONAL0.076
110J2489X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.54580.41071370.37392606274399
3.5458-3.59410.37561380.358626112749100
3.5941-3.64520.40211380.343926222760100
3.6452-3.69920.34321370.32426112748100
3.6992-3.75670.35221380.295126212759100
3.7567-3.81780.28921380.281326272765100
3.8178-3.88320.25841370.260825962733100
3.8832-3.95330.28281390.2526372776100
3.9533-4.02870.25511380.236826202758100
4.0287-4.11020.26041370.233126172754100
4.1102-4.19880.25741380.224926132751100
4.1988-4.29550.2561390.207226362775100
4.2955-4.40180.19661390.187626522791100
4.4018-4.51950.19761360.175625862722100
4.5195-4.65090.181390.168626362775100
4.6509-4.7990.19141400.162326562796100
4.799-4.9680.21621360.166825852721100
4.968-5.16360.19141390.172126522791100
5.1636-5.39410.23481380.174626142752100
5.3941-5.67230.21781400.183226542794100
5.6723-6.01850.20581370.178226072744100
6.0185-6.46840.19571400.204826572797100
6.4684-7.09260.25611380.227926362774100
7.0926-8.0590.23991400.192126452785100
8.059-9.93960.17621380.172726322770100
9.9396-19.93860.25211410.23952647278899

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