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- PDB-2xq7: Pentameric ligand gated ion channel GLIC in complex with cadmium ... -

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Basic information

Entry
Database: PDB / ID: 2xq7
TitlePentameric ligand gated ion channel GLIC in complex with cadmium ion (Cd2+)
ComponentsGLR4197 PROTEIN
KeywordsMEMBRANE PROTEIN / OPEN CHANNEL BLOCK
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
: / Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.4 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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)181,95110
Polymers181,3895
Non-polymers5625
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21380 Å2
ΔGint-179.1 kcal/mol
Surface area65540 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 / PENTAMERIC LIGAND GATED ION CHANNEL


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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd

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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: 5.16 Å3/Da / Density % sol: 76.2 % / Description: NONE
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG 4000, 50MM CH3COONA, 200MM (NH4)2SO4, PH 4.0, 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: 1.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 50052 / % possible obs: 87.1 % / Observed criterion σ(I): 3.1 / Redundancy: 3 % / Biso Wilson estimate: 93.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8

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Processing

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

Resolution: 3.4→40.2 Å / SU ML: 0.46 / σ(F): 1.89 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 2493 5 %
Rwork0.2421 --
obs0.2432 49894 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.241 Å2 / ksol: 0.263 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-30.222 Å20 Å2-46.7406 Å2
2---7.4799 Å20 Å2
3----22.742 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 5 0 12610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113015
X-RAY DIFFRACTIONf_angle_d1.33117785
X-RAY DIFFRACTIONf_dihedral_angle_d18.184659
X-RAY DIFFRACTIONf_chiral_restr0.0942066
X-RAY DIFFRACTIONf_plane_restr0.0052235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2530X-RAY DIFFRACTIONPOSITIONAL
12B2530X-RAY DIFFRACTIONPOSITIONAL0.051
13C2530X-RAY DIFFRACTIONPOSITIONAL0.036
14D2530X-RAY DIFFRACTIONPOSITIONAL0.039
15E2530X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.46540.4169860.35971923X-RAY DIFFRACTION72
3.4654-3.53610.34321450.34642627X-RAY DIFFRACTION99
3.5361-3.61290.38691330.3142696X-RAY DIFFRACTION99
3.6129-3.69690.37691190.30022607X-RAY DIFFRACTION99
3.6969-3.78930.31161610.28372648X-RAY DIFFRACTION99
3.7893-3.89160.26821350.26082667X-RAY DIFFRACTION100
3.8916-4.00610.26481520.24672682X-RAY DIFFRACTION100
4.0061-4.13520.25961430.23362652X-RAY DIFFRACTION100
4.1352-4.28290.24221320.2172699X-RAY DIFFRACTION100
4.2829-4.45410.24481310.20122680X-RAY DIFFRACTION100
4.4541-4.65660.20731670.1792641X-RAY DIFFRACTION99
4.6566-4.90170.22751280.16262670X-RAY DIFFRACTION100
4.9017-5.20820.17911290.1682695X-RAY DIFFRACTION100
5.2082-5.60930.21551750.18882677X-RAY DIFFRACTION100
5.6093-6.1720.27881590.22962659X-RAY DIFFRACTION100
6.172-7.06090.2714840.24662763X-RAY DIFFRACTION100
7.0609-8.88020.32671290.22962707X-RAY DIFFRACTION100
8.8802-40.20250.23581850.28852708X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.5775 Å / Origin y: 3.4938 Å / Origin z: 52.5921 Å
111213212223313233
T0.1414 Å20.0663 Å20.0534 Å2-0.1639 Å2-0.0457 Å2--0.2235 Å2
L0.4342 °2-0.1365 °20.1323 °2-0.5924 °2-0.1097 °2--0.642 °2
S0.0821 Å °0.0428 Å °-0.0184 Å °0.0431 Å °-0.0299 Å °-0.0404 Å °0.1127 Å °0.0984 Å °0 Å °
Refinement TLS groupSelection details: ALL

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