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- PDB-6f7a: Gloeobacter Ligand-gated Ion Channel (GLIC) closed state crystall... -

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Basic information

Entry
Database: PDB / ID: 6f7a
TitleGloeobacter Ligand-gated Ion Channel (GLIC) closed state crystallized in an ultra-swollen lipidic mesophase
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
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
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
Similarity search - Domain/homology
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6 Å
AuthorsMartiel, I. / Zabara, A. / Chong, J.Y.T. / Stark, L. / Cromer, B. / Dummond, C.J. / Mezzenga, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSinergia Grant CRSII2_154451 Switzerland
CitationJournal: Nat Commun / Year: 2018
Title: Design of ultra-swollen lipidic mesophases for the crystallization of membrane proteins with large extracellular domains.
Authors: Zabara, A. / Chong, J.T.Y. / Martiel, I. / Stark, L. / Cromer, B.A. / Speziale, C. / Drummond, C.J. / Mezzenga, R.
History
DepositionDec 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 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: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel


Theoretical massNumber of molelcules
Total (without water)178,2105
Polymers178,2105
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18070 Å2
ΔGint-177 kcal/mol
Surface area68830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 208.220, 255.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:10 or (resid 11 and (name...
21(chain B and (resseq 5:12 or (resid 13 and (name...
31(chain C and (resseq 5:10 or (resid 11 and (name...
41(chain D and (resseq 5:10 or (resid 11 and (name...
51(chain E and (resseq 5:10 or (resid 11 and (name...

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
11VALVALPROPRO(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 101 - 6
12ILEILEILEILE(chain A and (resseq 5:10 or (resid 11 and (name...AA117
13VALVALPHEPHE(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3151 - 311
14VALVALPHEPHE(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3151 - 311
15VALVALPHEPHE(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3151 - 311
16VALVALPHEPHE(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 3151 - 311
21VALVALALAALA(chain B and (resseq 5:12 or (resid 13 and (name...BB5 - 121 - 8
22ASPASPASPASP(chain B and (resseq 5:12 or (resid 13 and (name...BB139
23VALVALPHEPHE(chain B and (resseq 5:12 or (resid 13 and (name...BB5 - 3151 - 311
24VALVALPHEPHE(chain B and (resseq 5:12 or (resid 13 and (name...BB5 - 3151 - 311
25VALVALPHEPHE(chain B and (resseq 5:12 or (resid 13 and (name...BB5 - 3151 - 311
26VALVALPHEPHE(chain B and (resseq 5:12 or (resid 13 and (name...BB5 - 3151 - 311
31VALVALPROPRO(chain C and (resseq 5:10 or (resid 11 and (name...CC5 - 101 - 6
32ILEILEILEILE(chain C and (resseq 5:10 or (resid 11 and (name...CC117
33VALVALPHEPHE(chain C and (resseq 5:10 or (resid 11 and (name...CC5 - 3151 - 311
34VALVALPHEPHE(chain C and (resseq 5:10 or (resid 11 and (name...CC5 - 3151 - 311
35VALVALPHEPHE(chain C and (resseq 5:10 or (resid 11 and (name...CC5 - 3151 - 311
36VALVALPHEPHE(chain C and (resseq 5:10 or (resid 11 and (name...CC5 - 3151 - 311
41VALVALPROPRO(chain D and (resseq 5:10 or (resid 11 and (name...DD5 - 101 - 6
42ILEILEILEILE(chain D and (resseq 5:10 or (resid 11 and (name...DD117
43VALVALPHEPHE(chain D and (resseq 5:10 or (resid 11 and (name...DD5 - 3151 - 311
44VALVALPHEPHE(chain D and (resseq 5:10 or (resid 11 and (name...DD5 - 3151 - 311
45VALVALPHEPHE(chain D and (resseq 5:10 or (resid 11 and (name...DD5 - 3151 - 311
46VALVALPHEPHE(chain D and (resseq 5:10 or (resid 11 and (name...DD5 - 3151 - 311
51VALVALPROPRO(chain E and (resseq 5:10 or (resid 11 and (name...EE5 - 101 - 6
52ILEILEILEILE(chain E and (resseq 5:10 or (resid 11 and (name...EE117
53VALVALPHEPHE(chain E and (resseq 5:10 or (resid 11 and (name...EE5 - 3151 - 311
54VALVALPHEPHE(chain E and (resseq 5:10 or (resid 11 and (name...EE5 - 3151 - 311
55VALVALPHEPHE(chain E and (resseq 5:10 or (resid 11 and (name...EE5 - 3151 - 311
56VALVALPHEPHE(chain E and (resseq 5:10 or (resid 11 and (name...EE5 - 3151 - 311

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Components

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 35642.043 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase
Details: 0.2 M (NH4)SO4, 0.02M NaCl, 0.02M Na Act 4 pH, 33%v/v PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6→48.201 Å / Num. obs: 28508 / % possible obs: 98 % / Redundancy: 5.4 % / Biso Wilson estimate: 284.44 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.42 / Net I/σ(I): 4.99
Reflection shellResolution: 6→6.215 Å / Num. unique obs: 533 / CC1/2: 0.13

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NPQ

4npq


Resolution: 6→48.201 Å / SU ML: 1.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.3184 265 5.01 %
Rwork0.286 --
obs0.2878 5287 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 429.06 Å2 / Biso mean: 307.3586 Å2 / Biso min: 220.82 Å2
Refinement stepCycle: final / Resolution: 6→48.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11682 0 0 0 11682
Num. residues----1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712002
X-RAY DIFFRACTIONf_angle_d0.97316555
X-RAY DIFFRACTIONf_chiral_restr0.0562023
X-RAY DIFFRACTIONf_plane_restr0.0042090
X-RAY DIFFRACTIONf_dihedral_angle_d11.516979
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6448X-RAY DIFFRACTION5.844TORSIONAL
12B6448X-RAY DIFFRACTION5.844TORSIONAL
13C6448X-RAY DIFFRACTION5.844TORSIONAL
14D6448X-RAY DIFFRACTION5.844TORSIONAL
15E6448X-RAY DIFFRACTION5.844TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6-7.55460.40241310.358224872618100
7.5546-48.20250.29311340.26132535266997

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