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- PDB-6hk0: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 6hk0
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) F16'S pore mutant (F247S) with alternate M4 conformation.
ComponentsCys-loop ligand-gated ion channel
KeywordsMEMBRANE PROTEIN / ion channel / pentameric ligand-gated ion channel / cya-loop receptor
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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsNury, H. / Spurny, R. / Govaerts, C. / Evans, G.L. / Pardon, E. / Steyaert, J. / Ulens, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel.
Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. ...Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. / Nury, H. / Steyaert, J. / Baenziger, J.E. / Ulens, C.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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.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

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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)358,66920
Polymers353,56310
Non-polymers5,10610
Water00
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)179,33410
Polymers176,7815
Non-polymers2,5535
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-151 kcal/mol
Surface area67130 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)179,33410
Polymers176,7815
Non-polymers2,5535
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27390 Å2
ΔGint-155 kcal/mol
Surface area66560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.800, 264.697, 111.185
Angle α, β, γ (deg.)90.000, 108.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 286 or resid 293 through 297))
21(chain B and (resid 11 through 286 or resid 293 through 297))
31(chain C and (resid 11 through 286 or resid 293 through 297))
41(chain D and (resid 11 through 286 or resid 293 through 297))
51(chain E and (resid 11 through 286 or resid 293 through 297))
61(chain F and (resid 11 through 286 or resid 293 through 297))
71(chain G and (resid 11 through 286 or resid 293 through 297))
81(chain H and (resid 11 through 286 or resid 293 through 297))
91(chain I and (resid 11 through 286 or resid 293 through 297))
101(chain J and resid 11 through 297)

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
11PROPROARGARG(chain A and (resid 11 through 286 or resid 293 through 297))AA11 - 2861 - 276
12ASPASPILEILE(chain A and (resid 11 through 286 or resid 293 through 297))AA293 - 297283 - 287
21PROPROARGARG(chain B and (resid 11 through 286 or resid 293 through 297))BB11 - 2861 - 276
22ASPASPILEILE(chain B and (resid 11 through 286 or resid 293 through 297))BB293 - 297283 - 287
31PROPROARGARG(chain C and (resid 11 through 286 or resid 293 through 297))CC11 - 2861 - 276
32ASPASPILEILE(chain C and (resid 11 through 286 or resid 293 through 297))CC293 - 297283 - 287
41PROPROARGARG(chain D and (resid 11 through 286 or resid 293 through 297))DD11 - 2861 - 276
42ASPASPILEILE(chain D and (resid 11 through 286 or resid 293 through 297))DD293 - 297283 - 287
51PROPROARGARG(chain E and (resid 11 through 286 or resid 293 through 297))EE11 - 2861 - 276
52ASPASPILEILE(chain E and (resid 11 through 286 or resid 293 through 297))EE293 - 297283 - 287
61PROPROARGARG(chain F and (resid 11 through 286 or resid 293 through 297))FF11 - 2861 - 276
62ASPASPILEILE(chain F and (resid 11 through 286 or resid 293 through 297))FF293 - 297283 - 287
71PROPROARGARG(chain G and (resid 11 through 286 or resid 293 through 297))GG11 - 2861 - 276
72ASPASPILEILE(chain G and (resid 11 through 286 or resid 293 through 297))GG293 - 297283 - 287
81PROPROARGARG(chain H and (resid 11 through 286 or resid 293 through 297))HH11 - 2861 - 276
82ASPASPILEILE(chain H and (resid 11 through 286 or resid 293 through 297))HH293 - 297283 - 287
91PROPROARGARG(chain I and (resid 11 through 286 or resid 293 through 297))II11 - 2861 - 276
92ASPASPILEILE(chain I and (resid 11 through 286 or resid 293 through 297))II293 - 297283 - 287
101PROPROILEILE(chain J and resid 11 through 297)JJ11 - 2971 - 287

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Components

#1: Protein
Cys-loop ligand-gated ion channel / ELIC


Mass: 35356.258 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate, 50 mM ADA pH 6.5, 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→48.9 Å / Num. obs: 75824 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.089 / Rrim(I) all: 0.177 / Net I/av σ(I): 6.7 / Net I/σ(I): 6.7
Reflection shellResolution: 3.45→3.52 Å / Rmerge(I) obs: 1.365 / Mean I/σ(I) obs: 1 / Num. unique obs: 4508 / CC1/2: 0.409 / Rpim(I) all: 0.903 / Rrim(I) all: 1.834

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yoe

2yoe


Resolution: 3.45→19.991 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.75
RfactorNum. reflection% reflection
Rfree0.2655 3749 4.98 %
Rwork0.2278 --
obs0.2298 75338 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 299.32 Å2 / Biso mean: 112.7414 Å2 / Biso min: 44.85 Å2
Refinement stepCycle: final / Resolution: 3.45→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24972 0 240 0 25212
Biso mean--150.71 --
Num. residues----3064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8530X-RAY DIFFRACTION3.435TORSIONAL
12B8530X-RAY DIFFRACTION3.435TORSIONAL
13C8530X-RAY DIFFRACTION3.435TORSIONAL
14D8530X-RAY DIFFRACTION3.435TORSIONAL
15E8530X-RAY DIFFRACTION3.435TORSIONAL
16F8530X-RAY DIFFRACTION3.435TORSIONAL
17G8530X-RAY DIFFRACTION3.435TORSIONAL
18H8530X-RAY DIFFRACTION3.435TORSIONAL
19I8530X-RAY DIFFRACTION3.435TORSIONAL
110J8530X-RAY DIFFRACTION3.435TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.45-3.49340.38211440.366326572801100
3.4934-3.53920.3991280.357326622790100
3.5392-3.58740.36041150.343326752790100
3.5874-3.63830.35521320.325726302762100
3.6383-3.69230.36771210.319326602781100
3.6923-3.74960.31121200.309826702790100
3.7496-3.81070.34491350.302926732808100
3.8107-3.87590.32531290.281726112740100
3.8759-3.94590.32471360.280326932829100
3.9459-4.02120.28551400.26426222762100
4.0212-4.10260.32031370.256226712808100
4.1026-4.1910.25951210.250626652786100
4.191-4.28750.29741280.223526542782100
4.2875-4.39370.25211480.213326432791100
4.3937-4.51110.23721460.200926162762100
4.5111-4.64230.23051560.19726652821100
4.6423-4.79010.24821260.184526402766100
4.7901-4.95880.26931590.203926132772100
4.9588-5.15410.27121470.205526352782100
5.1541-5.38430.29061480.199226712819100
5.3843-5.66210.22021500.203926462796100
5.6621-6.00780.24431570.20926322789100
6.0078-6.45710.30471610.23226312792100
6.4571-7.08050.31071430.233326892832100
7.0805-8.04610.28051270.210726622789100
8.0461-9.92620.18031460.16822645279199
9.9262-19.9910.21551490.20222658280799
Refinement TLS params.Method: refined / Origin x: -93.8686 Å / Origin y: -76.9074 Å / Origin z: -40.6466 Å
111213212223313233
T0.6359 Å2-0.0334 Å2-0.1578 Å2-0.6 Å2-0.0525 Å2--0.3972 Å2
L0.2329 °2-0.2095 °2-0.1408 °2-0.9463 °2-0.2001 °2--0.267 °2
S-0.0245 Å °-0.0342 Å °-0.001 Å °-0.0266 Å °0.0677 Å °-0.0739 Å °-0.0666 Å °-0.0375 Å °-0.043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 317
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allB11 - 317
4X-RAY DIFFRACTION1allB401
5X-RAY DIFFRACTION1allC11 - 317
6X-RAY DIFFRACTION1allC401
7X-RAY DIFFRACTION1allD11 - 317
8X-RAY DIFFRACTION1allD401
9X-RAY DIFFRACTION1allE11 - 317
10X-RAY DIFFRACTION1allE401
11X-RAY DIFFRACTION1allF11 - 317
12X-RAY DIFFRACTION1allF401
13X-RAY DIFFRACTION1allG11 - 317
14X-RAY DIFFRACTION1allG401
15X-RAY DIFFRACTION1allH11 - 317
16X-RAY DIFFRACTION1allH401
17X-RAY DIFFRACTION1allI11 - 317
18X-RAY DIFFRACTION1allI401
19X-RAY DIFFRACTION1allJ11 - 317
20X-RAY DIFFRACTION1allJ401

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