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- PDB-6v4a: An open conformation of a Pentameic ligand-gated ion channel with... -

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Basic information

Entry
Database: PDB / ID: 6v4a
TitleAn open conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain
ComponentsNeur_chan_LBD domain-containing protein
KeywordsTRANSPORT PROTEIN / Pentameric ligand-gated ion channel
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane
Similarity search - Function
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
Similarity search - Domain/homology
PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL / Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
Similarity search - Component
Biological speciesuncultured Desulfofustis sp. PB-SRB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.83 Å
AuthorsDelarue, M. / Hu, H.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel.
Authors: Hu, H. / Howard, R.J. / Bastolla, U. / Lindahl, E. / Delarue, M.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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: Neur_chan_LBD domain-containing protein
E: Neur_chan_LBD domain-containing protein
D: Neur_chan_LBD domain-containing protein
C: Neur_chan_LBD domain-containing protein
B: Neur_chan_LBD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,64615
Polymers358,6705
Non-polymers4,97610
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27190 Å2
ΔGint-57 kcal/mol
Surface area132210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.064, 116.028, 169.630
Angle α, β, γ (deg.)90.000, 109.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12A
22D
13A
23C
14A
24B
15E
25D
16E
26C
17E
27B
18D
28C
19D
29B
110C
210B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 36 - 636 / Label seq-ID: 36 - 636

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21EB
12AA
22DC
13AA
23CD
14AA
24BE
15EB
25DC
16EB
26CD
17EB
27BE
18DC
28CD
19DC
29BE
110CD
210BE

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Neur_chan_LBD domain-containing protein


Mass: 71733.992 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Desulfofustis sp. PB-SRB1 (bacteria)
Gene: N839_03575 / Production host: Escherichia coli (E. coli) / References: UniProt: V4JF97
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-P3A / PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL


Mass: 872.997 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C41H78O15P2 / Comment: phospholipid*YM
Has ligand of interestN

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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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.3 M NH4-Formate, 0.1 M Tris 7.5, 30% (v/v) PEG-MME 500

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.83→48.61 Å / Num. obs: 49576 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 7.6
Reflection shellResolution: 3.83→3.93 Å / Num. unique obs: 3486 / CC1/2: 0.448

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FLI

6fli


Resolution: 3.83→25 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.839 / SU B: 152.957 / SU ML: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2914 1876 5.1 %RANDOM
Rwork0.2556 ---
obs0.2574 34738 73.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 356.56 Å2 / Biso mean: 145.969 Å2 / Biso min: 25.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å2-0 Å2-0.44 Å2
2--4.66 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 3.83→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23051 0 142 0 23193
Biso mean--202.15 --
Num. residues----2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01923711
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221764
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.96432281
X-RAY DIFFRACTIONr_angle_other_deg1.169350314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46352940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31324.2541093
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.221153718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.98515132
X-RAY DIFFRACTIONr_chiral_restr0.1340.23673
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02126466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024978
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A362200.04
12E362200.04
21A361240.04
22D361240.04
31A362020.04
32C362020.04
41A362340.04
42B362340.04
51E363680.04
52D363680.04
61E363860.04
62C363860.04
71E360460.04
72B360460.04
81D364780.04
82C364780.04
91D360900.05
92B360900.05
101C362140.04
102B362140.04
LS refinement shellResolution: 3.835→3.932 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 64 -
Rwork0.327 985 -
all-1049 -
obs--29.2 %
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)
18.33111.01640.40461.84650.02891.4399-0.1335-1.03270.25580.7310.2518-0.3504-0.31730.1227-0.11830.80750.4115-0.18870.4414-0.21660.1922-66.13413.85665.113
26.87670.8158-0.81991.899-0.05421.88540.02620.16021.35560.08590.0088-0.3463-0.8770.2016-0.0350.76720.0768-0.24020.1373-0.02450.514-66.52328.03934.544
37.56670.0006-1.15271.959-0.03591.6313-0.10721.08580.2044-0.5370.1481-0.4137-0.11590.1084-0.04090.5563-0.1412-0.01590.3529-0.04160.1592-66.9193.39311.478
47.3348-1.121-0.64431.5505-0.19071.9373-0.14710.5344-1.1078-0.1885-0.0227-0.17220.69860.13950.16980.608-0.05830.2580.1169-0.22440.6096-66.962-26.47727.838
57.3918-0.66060.90441.3718-0.12671.5591-0.2037-0.634-1.06190.44930.0708-0.05060.44640.30390.13290.76250.37030.2770.26230.25920.3112-66.347-19.71461.339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 195
2X-RAY DIFFRACTION1A199 - 311
3X-RAY DIFFRACTION1A321 - 514
4X-RAY DIFFRACTION1A515 - 636
5X-RAY DIFFRACTION2B36 - 195
6X-RAY DIFFRACTION2B199 - 311
7X-RAY DIFFRACTION2B321 - 514
8X-RAY DIFFRACTION2B515 - 636
9X-RAY DIFFRACTION3C36 - 195
10X-RAY DIFFRACTION3C199 - 311
11X-RAY DIFFRACTION3C312 - 514
12X-RAY DIFFRACTION3C515 - 636
13X-RAY DIFFRACTION4D36 - 195
14X-RAY DIFFRACTION4D200 - 311
15X-RAY DIFFRACTION4D312 - 514
16X-RAY DIFFRACTION4D515 - 636
17X-RAY DIFFRACTION5E36 - 195
18X-RAY DIFFRACTION5E200 - 311
19X-RAY DIFFRACTION5E312 - 514
20X-RAY DIFFRACTION5E515 - 636

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