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- PDB-2xq8: Pentameric ligand gated ion channel GLIC in complex with zinc ion... -

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Basic information

Entry
Database: PDB / ID: 2xq8
TitlePentameric ligand gated ion channel GLIC in complex with zinc ion (Zn2+)
ComponentsGLR4197 PROTEIN
KeywordsMEMBRANE PROTEIN / OPEN CHANNEL BLOCK
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.6 Å
AuthorsHilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Basis of Open Channel Block in a Prokaryotic Pentameric Ligand-Gated Ion Channel
Authors: Hilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
#1: Journal: Nature / Year: 2009
Title: Structure of a Potentially Open State of a Proton-Activated Pentameric Ligand-Gated Ion Channel.
Authors: Hilf, R.J.C. / Dutzler, R.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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)181,5858
Polymers181,3895
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-201 kcal/mol
Surface area64430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.314, 128.310, 164.374
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:316 )
211CHAIN B AND (RESSEQ 7:316 )
311CHAIN C AND (RESSEQ 7:316 )
411CHAIN D AND (RESSEQ 7:316 )
511CHAIN E AND (RESSEQ 7:316 )

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Components

#1: Protein
GLR4197 PROTEIN / GLIC


Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: RESIDUES 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 5.29 Å3/Da / Density % sol: 76.58 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG4000, 50MM CH3COONA, 200MM (NH4)2SO4, PH4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
ReflectionResolution: 3.6→39.72 Å / Num. obs: 54863 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.6→40.2 Å / SU ML: 0.57 / σ(F): 1.91 / Phase error: 28.29 / Stereochemistry target values: ML / Details: RESIDUES 1-6 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2485 2167 5.1 %
Rwork0.238 --
obs0.2385 42935 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.379 Å2 / ksol: 0.264 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.0635 Å2-0 Å2-51.0984 Å2
2---15.9122 Å20 Å2
3----7.1513 Å2
Refinement stepCycle: LAST / Resolution: 3.6→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 3 0 12608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112995
X-RAY DIFFRACTIONf_angle_d1.45717760
X-RAY DIFFRACTIONf_dihedral_angle_d17.0094650
X-RAY DIFFRACTIONf_chiral_restr0.0892065
X-RAY DIFFRACTIONf_plane_restr0.0062230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2530X-RAY DIFFRACTIONPOSITIONAL
12B2530X-RAY DIFFRACTIONPOSITIONAL0.06
13C2530X-RAY DIFFRACTIONPOSITIONAL0.047
14D2530X-RAY DIFFRACTIONPOSITIONAL0.055
15E2530X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.595-3.67860.34151270.31262613X-RAY DIFFRACTION97
3.6786-3.77050.35951630.29182695X-RAY DIFFRACTION100
3.7705-3.87240.31311440.28832730X-RAY DIFFRACTION100
3.8724-3.98630.37021380.26292734X-RAY DIFFRACTION100
3.9863-4.11480.2811450.23992696X-RAY DIFFRACTION100
4.1148-4.26170.23791430.22932704X-RAY DIFFRACTION100
4.2617-4.43210.2531340.21552723X-RAY DIFFRACTION100
4.4321-4.63360.21041650.19332713X-RAY DIFFRACTION100
4.6336-4.87750.22281310.17562719X-RAY DIFFRACTION100
4.8775-5.18250.19321340.17642710X-RAY DIFFRACTION100
5.1825-5.58160.22261730.20792719X-RAY DIFFRACTION100
5.5816-6.14160.29921650.23152714X-RAY DIFFRACTION100
6.1416-7.02620.2698790.2292805X-RAY DIFFRACTION100
7.0262-8.83670.27491410.21912742X-RAY DIFFRACTION100
8.8367-40.20220.16581850.27932751X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.8447 Å / Origin y: 3.9327 Å / Origin z: 52.467 Å
111213212223313233
T0.04 Å2-0.0706 Å20.0661 Å2-0.0964 Å20.0392 Å2--0.0214 Å2
L0.5248 °20.0301 °20.1058 °2-0.7448 °20.1177 °2--0.5873 °2
S0.0213 Å °0.1367 Å °0.0104 Å °-0.0095 Å °-0.0644 Å °0.034 Å °-0.0502 Å °-0.02 Å °-0.0005 Å °
Refinement TLS groupSelection details: ALL

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