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- PDB-3eam: An open-pore structure of a bacterial pentameric ligand-gated ion... -

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Basic information

Entry
Database: PDB / ID: 3eam
TitleAn open-pore structure of a bacterial pentameric ligand-gated ion channel
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / pentameric ligand-gated ion-channel
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsBocquet, N. / Nury, H. / Baaden, M. / Le Poupon, C. / Changeux, J.P. / Delarue, M. / Corringer, P.J.
CitationJournal: Nature / Year: 2009
Title: X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation.
Authors: Bocquet, N. / Nury, H. / Baaden, M. / Le Poupon, C. / Changeux, J.P. / Delarue, M. / Corringer, P.J.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
D: Glr4197 protein
E: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,37526
Polymers181,4595
Non-polymers14,91621
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42130 Å2
ΔGint-252 kcal/mol
Surface area60970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.320, 133.640, 160.180
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12A
22C
32D
42E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALLEULEU1AA5 - 525 - 52
211VALVALLEULEU1BB5 - 525 - 52
311VALVALLEULEU1CC5 - 525 - 52
411VALVALLEULEU1DD5 - 525 - 52
511VALVALLEULEU1EE5 - 525 - 52
121TYRTYRALAALA1AA66 - 8766 - 87
221TYRTYRALAALA1BB66 - 8766 - 87
321TYRTYRALAALA1CC66 - 8766 - 87
421TYRTYRALAALA1DD66 - 8766 - 87
521TYRTYRALAALA1EE66 - 8766 - 87
131VALVALSERSER1AA89 - 9589 - 95
231VALVALSERSER1BB89 - 9589 - 95
331VALVALSERSER1CC89 - 9589 - 95
431VALVALSERSER1DD89 - 9589 - 95
531VALVALSERSER1EE89 - 9589 - 95
141GLYGLYARGARG1AA98 - 13898 - 138
241GLYGLYARGARG1BB98 - 13898 - 138
341GLYGLYARGARG1CC98 - 13898 - 138
441GLYGLYARGARG1DD98 - 13898 - 138
541GLYGLYARGARG1EE98 - 13898 - 138
151ASNASNGLUGLU2AA139 - 147139 - 147
251ASNASNGLUGLU2BB139 - 147139 - 147
351ASNASNGLUGLU2CC139 - 147139 - 147
451ASNASNGLUGLU2DD139 - 147139 - 147
551ASNASNGLUGLU2EE139 - 147139 - 147
161LYSLYSTYRTYR1AA148 - 221148 - 221
261LYSLYSTYRTYR1BB148 - 221148 - 221
361LYSLYSTYRTYR1CC148 - 221148 - 221
461LYSLYSTYRTYR1DD148 - 221148 - 221
561LYSLYSTYRTYR1EE148 - 221148 - 221
171ALAALAPHEPHE1AA223 - 315223 - 315
271ALAALAPHEPHE1BB223 - 315223 - 315
371ALAALAPHEPHE1CC223 - 315223 - 315
471ALAALAPHEPHE1DD223 - 315223 - 315
571ALAALAPHEPHE1EE223 - 315223 - 315
112SERSERGLYGLY1AA95 - 9895 - 98
212SERSERGLYGLY1CC95 - 9895 - 98
312SERSERGLYGLY1DD95 - 9895 - 98
412SERSERGLYGLY1EE95 - 9895 - 98

NCS ensembles :
ID
1
2

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Components

#1: Protein
Glr4197 protein


Mass: 36291.750 Da / Num. of mol.: 5 / Fragment: UNP residues 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q7NDN8
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 5.27 Å3/Da / Density % sol: 76.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, NH4SCN, NaAc, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 83260 / Redundancy: 3.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.34
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.05

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0073refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.807 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 4063 5 %RANDOM
Rwork0.19885 ---
obs0.20046 77236 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-6 Å2
2--0.43 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 769 111 13505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02213729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0342.00918647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10751550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54822.931580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.272152075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1611590
X-RAY DIFFRACTIONr_chiral_restr0.1180.22158
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.57875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7212895
X-RAY DIFFRACTIONr_scbond_it2.76535854
X-RAY DIFFRACTIONr_scangle_it4.9964.55752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2362tight positional0.080.05
11B2362tight positional0.090.05
11C2362tight positional0.070.05
11D2362tight positional0.070.05
11E2362tight positional0.060.05
22A25tight positional0.040.05
22C25tight positional0.050.05
22D25tight positional0.040.05
22E25tight positional0.030.05
11A32medium positional0.110.5
11B32medium positional0.110.5
11C32medium positional0.110.5
11D32medium positional0.10.5
11E32medium positional0.120.5
11A2362tight thermal0.130.5
11B2362tight thermal0.140.5
11C2362tight thermal0.130.5
11D2362tight thermal0.130.5
11E2362tight thermal0.130.5
22A25tight thermal0.130.5
22C25tight thermal0.10.5
22D25tight thermal0.080.5
22E25tight thermal0.090.5
11A32medium thermal0.142
11B32medium thermal0.132
11C32medium thermal0.162
11D32medium thermal0.162
11E32medium thermal0.152
LS refinement shellResolution: 2.9→2.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 291 -
Rwork0.32 5324 -
obs--99.84 %

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