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- PDB-6v4s: A Closed pore conformation of a Pentameic ligand-gated ion channe... -

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Basic information

Entry
Database: PDB / ID: 6v4s
TitleA Closed pore 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 / homologyextracellular ligand-gated monoatomic ion channel activity / 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 / transmembrane signaling receptor activity / membrane / Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
Function and homology information
Biological speciesuncultured Desulfofustis sp. PB-SRB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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 29, 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)364,31532
Polymers358,6705
Non-polymers5,64527
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36040 Å2
ΔGint-371 kcal/mol
Surface area130520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.406, 337.254, 111.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 35 - 639 / Label seq-ID: 35 - 639

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

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Protein / Sugars , 2 types, 15 molecules AEDCB

#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
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 22 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.5 Å3/Da / Density % sol: 72.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 7.5, 250 mM CaCl2, 14.5% (w/v) PEG-MME 2000

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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: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.55→48.18 Å / Num. obs: 73420 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 11
Reflection shellResolution: 3.55→3.64 Å / Redundancy: 12.7 % / Num. unique obs: 5125 / CC1/2: 0.372 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VL0, 4HFI

2vl0

4hfi


Resolution: 3.55→48.04 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 83.933 / SU ML: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.615
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 3250 5 %RANDOM
Rwork0.1935 ---
obs0.1972 62330 88.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 319.72 Å2 / Biso mean: 140.679 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--10.69 Å2-0 Å20 Å2
2--18.68 Å2-0 Å2
3----7.99 Å2
Refinement stepCycle: final / Resolution: 3.55→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22983 0 268 5 23256
Biso mean--195.88 105.66 -
Num. residues----2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01923775
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221744
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.96832366
X-RAY DIFFRACTIONr_angle_other_deg1.224350300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.99852921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77424.1661097
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.95153706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.80315135
X-RAY DIFFRACTIONr_chiral_restr0.1380.23746
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02126354
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024997
X-RAY DIFFRACTIONr_rigid_bond_restr2.033345519
X-RAY DIFFRACTIONr_sphericity_free83.697515
X-RAY DIFFRACTIONr_sphericity_bonded41.827544989
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A358740.07
12E358740.07
21A360680.06
22D360680.06
31A357080.07
32C357080.07
41A359580.06
42B359580.06
51E363440.06
52D363440.06
61E360680.07
62C360680.07
71E359600.07
72B359600.07
81D364040.06
82C364040.06
91D363180.06
92B363180.06
101C361800.06
102B361800.06
LS refinement shellResolution: 3.551→3.643 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 115 -
Rwork0.366 2226 -
all-2341 -
obs--43.83 %
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)
11.40060.54250.13924.7294-0.28440.6829-0.13150.50360.7403-0.97930.1528-0.057-0.44350.096-0.02130.86920.00050.11690.21030.23650.57211.275415.748224.455
20.63480.4-0.14072.516-0.0990.9347-0.0192-0.05560.3661-0.16250.0792-0.2855-0.59670.2923-0.060.708-0.1440.00060.1071-0.03340.599729.643416.455253.864
30.90560.57360.11492.24650.5440.8103-0.0434-0.24740.55710.13470.08520.085-0.41570.0594-0.04190.6162-0.0044-0.00430.1044-0.16530.53377.771416.773280.385
40.6337-0.251-0.11514.18270.6991.0568-0.0306-0.15090.44140.19570.02620.4703-0.5351-0.2560.00440.48760.1535-0.00820.1232-0.09950.5822-24.889416.898268.028
51.311-0.7941-0.02574.5331-0.190.6886-0.04120.28770.5809-0.49760.07220.2895-0.515-0.2449-0.0310.76290.1363-0.14920.16650.12410.4844-23.071416.132232.484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 196
2X-RAY DIFFRACTION1A200 - 307
3X-RAY DIFFRACTION1A322 - 514
4X-RAY DIFFRACTION1A515 - 639
5X-RAY DIFFRACTION2B35 - 196
6X-RAY DIFFRACTION2B200 - 308
7X-RAY DIFFRACTION2B320 - 514
8X-RAY DIFFRACTION2B515 - 639
9X-RAY DIFFRACTION3C35 - 196
10X-RAY DIFFRACTION3C201 - 311
11X-RAY DIFFRACTION3C321 - 514
12X-RAY DIFFRACTION3C515 - 639
13X-RAY DIFFRACTION4D35 - 196
14X-RAY DIFFRACTION4D200 - 311
15X-RAY DIFFRACTION4D319 - 514
16X-RAY DIFFRACTION4D515 - 639
17X-RAY DIFFRACTION5E35 - 196
18X-RAY DIFFRACTION5E200 - 311
19X-RAY DIFFRACTION5E319 - 514
20X-RAY DIFFRACTION5E515 - 639

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