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- PDB-4a98: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 4a98
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromoflurazepam
ComponentsCYS-LOOP LIGAND-GATED ION CHANNEL
KeywordsTRANSPORT PROTEIN / CYS-LOOP RECEPTOR / GABA-A RECEPTOR / BENZODIAZEPINE
Function / homology
Function and homology information


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 / 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
Chem-BFZ / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsSpurny, R. / Brams, M. / Nury, H. / Legrand, P. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Pentameric Ligand-Gated Ion Channel Elic is Activated by Gaba and Modulated by Benzodiazepines.
Authors: Spurny, R. / Ramerstorfer, J. / Price, K. / Brams, M. / Ernst, M. / Nury, H. / Verheij, M. / Legrand, P. / Bertrand, D. / Bertrand, S. / Dougherty, D.A. / De Esch, I.J.P. / Corringer, P. / ...Authors: Spurny, R. / Ramerstorfer, J. / Price, K. / Brams, M. / Ernst, M. / Nury, H. / Verheij, M. / Legrand, P. / Bertrand, D. / Bertrand, S. / Dougherty, D.A. / De Esch, I.J.P. / Corringer, P. / Sieghart, W. / Lummis, S.C.R. / Ulens, C.
History
DepositionNov 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_leaving_atom_flag / _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: CYS-LOOP LIGAND-GATED ION CHANNEL
B: CYS-LOOP LIGAND-GATED ION CHANNEL
C: CYS-LOOP LIGAND-GATED ION CHANNEL
D: CYS-LOOP LIGAND-GATED ION CHANNEL
E: CYS-LOOP LIGAND-GATED ION CHANNEL
F: CYS-LOOP LIGAND-GATED ION CHANNEL
G: CYS-LOOP LIGAND-GATED ION CHANNEL
H: CYS-LOOP LIGAND-GATED ION CHANNEL
I: CYS-LOOP LIGAND-GATED ION CHANNEL
J: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,15720
Polymers353,83410
Non-polymers4,32310
Water0
1
A: CYS-LOOP LIGAND-GATED ION CHANNEL
B: CYS-LOOP LIGAND-GATED ION CHANNEL
C: CYS-LOOP LIGAND-GATED ION CHANNEL
D: CYS-LOOP LIGAND-GATED ION CHANNEL
E: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,07810
Polymers176,9175
Non-polymers2,1625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-154.9 kcal/mol
Surface area65390 Å2
MethodPISA
2
F: CYS-LOOP LIGAND-GATED ION CHANNEL
G: CYS-LOOP LIGAND-GATED ION CHANNEL
H: CYS-LOOP LIGAND-GATED ION CHANNEL
I: CYS-LOOP LIGAND-GATED ION CHANNEL
J: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,07810
Polymers176,9175
Non-polymers2,1625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-150.7 kcal/mol
Surface area65570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.400, 268.200, 111.400
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CYS-LOOP LIGAND-GATED ION CHANNEL / ELIC


Mass: 35383.367 Da / Num. of mol.: 10 / Fragment: RESIDUES 11-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C7B7
#2: Chemical
ChemComp-BFZ / 7-BROMO-1-[2-(DIETHYLAMINO)ETHYL]-5-(2-FLUOROPHENYL)-1,3-DIHYDRO-2H-1,4-BENZODIAZEPIN-2-ONE / BROMOFLURAZEPAM


Mass: 432.329 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H23BrFN3O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.19 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91936
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91936 Å / Relative weight: 1
ReflectionResolution: 3.61→44.63 Å / Num. obs: 67378 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 11.4 % / Biso Wilson estimate: 93.73 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.61→25.47 Å / Cor.coef. Fo:Fc: 0.9031 / Cor.coef. Fo:Fc free: 0.8961 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 3412 5.07 %RANDOM
Rwork0.2306 ---
obs0.2314 67357 --
Displacement parametersBiso mean: 137.91 Å2
Baniso -1Baniso -2Baniso -3
1--14.2009 Å20 Å2-11.3481 Å2
2--14.6163 Å20 Å2
3----0.4154 Å2
Refine analyzeLuzzati coordinate error obs: 0.986 Å
Refinement stepCycle: LAST / Resolution: 3.61→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24850 0 270 0 25120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00825820HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9135210HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11420SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes670HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3780HARMONIC5
X-RAY DIFFRACTIONt_it25820HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion3.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3370SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28258SEMIHARMONIC4
LS refinement shellResolution: 3.61→3.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3075 244 5.25 %
Rwork0.2666 4407 -
all0.2687 4651 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6257-0.4061-0.62521.16630.75244.5809-0.0380.0565-0.30980.28450.21140.4850.2361-0.6495-0.17340.0582-0.08030.2286-0.06040.1119-0.2024-125.1419-51.1803-44.2025
20.9765-0.7124-1.71512.58581.4575.96360.1322-0.1733-0.11770.15880.2287-0.1170.26760.0047-0.361-0.10420.0260.0965-0.46330.0581-0.1847-104.7273-62.8273-39.9711
31.0545-0.3693-1.39871.7630.43256.01840.143-0.19720.1090.05750.1309-0.5374-0.05130.3948-0.2738-0.26140.05290.0772-0.2935-0.0984-0.1172-86.7023-47.3138-42.1779
41.2348-0.1612-0.70641.20450.47787.44410.1407-0.01480.3282-0.04180.0987-0.2557-0.3487-0.2599-0.23940.10770.10530.284-0.4864-0.0209-0.1256-95.9815-25.9142-47.6673
50.1829-0.05330.33391.54661.09316.76190.11810.05770.06620.09510.08650.3046-0.1577-0.5871-0.2046-0.01380.2480.31060.1180.1028-0.2281-119.8503-28.2972-48.9815
65.43731.3378-0.10131.139601.0019-0.1596-0.58260.00280.20520.0268-0.31660.22050.12210.1328-0.30180.13020.1673-0.115-0.01270.182-81.6868-119.43-17.9435
77.63581.48880.98361.67190.19741.0249-0.1805-0.0238-0.0689-0.2374-0.0397-0.27480.32380.20.2202-0.14270.01640.2949-0.41460.00210.0694-78.0294-129.977-39.0804
84.9164-0.18890.7261.6132-0.0630.8383-0.25710.52160.3294-0.60710.048-0.34010.01370.08820.20910.0157-0.16440.3253-0.34380.0336-0.0863-80.7684-113.464-56.1699
96.39030.4093-0.61861.6712-0.23750.9673-0.2811-0.380.3978-0.11320.1488-0.1644-0.3094-0.03160.1323-0.2301-0.04740.0653-0.573-0.01940.1487-86.0723-92.648-45.6492
106.3311.3182-0.9481.7483-0.41050.7079-0.1862-0.75040.14120.38450.0497-0.2634-0.22710.130.1365-0.2460.06590.0784-0.1038-0.2535-0.0077-86.6357-96.3314-21.9107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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