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- PDB-4chw: The electron crystallography structure of the cAMP-free potassium... -

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Basic information

Entry
Database: PDB / ID: 4chw
TitleThe electron crystallography structure of the cAMP-free potassium channel MloK1
ComponentsCYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241
KeywordsTRANSPORT PROTEIN / 2DX / VOLTAGE GATED POTASSIUM CHANNEL / CNBD / 2D CRYSTAL
Function / homology
Function and homology information


potassium channel activity / cAMP binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMESORHIZOBIUM LOTI (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 7 Å
AuthorsKowal, J. / Chami, M. / Baumgartner, P. / Arheit, M. / Chiu, P.L. / Rangl, M. / Scheuring, S. / Schroeder, G.F. / Nimigean, C.M. / Stahlberg, H.
CitationJournal: Nat Commun / Year: 2014
Title: Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1.
Authors: Julia Kowal / Mohamed Chami / Paul Baumgartner / Marcel Arheit / Po-Lin Chiu / Martina Rangl / Simon Scheuring / Gunnar F Schröder / Crina M Nimigean / Henning Stahlberg /
Abstract: Cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. The molecular determinants of ligand gating in these channels are still unknown, mainly ...Cyclic nucleotide-modulated ion channels are important for signal transduction and pacemaking in eukaryotes. The molecular determinants of ligand gating in these channels are still unknown, mainly because of a lack of direct structural information. Here we report ligand-induced conformational changes in full-length MloK1, a cyclic nucleotide-modulated potassium channel from the bacterium Mesorhizobium loti, analysed by electron crystallography and atomic force microscopy. Upon cAMP binding, the cyclic nucleotide-binding domains move vertically towards the membrane, and directly contact the S1-S4 voltage sensor domains. This is accompanied by a significant shift and tilt of the voltage sensor domain helices. In both states, the inner pore-lining helices are in an 'open' conformation. We propose a mechanism in which ligand binding can favour pore opening via a direct interaction between the cyclic nucleotide-binding domains and voltage sensors. This offers a simple mechanistic hypothesis for the coupling between ligand gating and voltage sensing in eukaryotic HCN channels.
History
DepositionDec 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Apr 24, 2019Group: Data collection / Other
Category: diffrn_radiation / diffrn_radiation_wavelength ...diffrn_radiation / diffrn_radiation_wavelength / pdbx_database_proc / pdbx_database_status
Item: _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wt / _pdbx_database_status.author_approval_type
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wt / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: CYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241
B: CYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241
C: CYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241
D: CYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,4596
Polymers154,3814
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.300, 105.300, 105.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CYCLIC NUCLEOTIDE-GATED POTASSIUM CHANNEL MLL3241 / MLOTIK1 CHANNEL / MLOK1


Mass: 38595.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CAMP NOT PRESENT IN BUFFER / Source: (gene. exp.) MESORHIZOBIUM LOTI (bacteria) / Plasmid: PASK90 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q98GN8
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: MLOK1 WITHOUT CAMP / Type: COMPLEX
Buffer solutionName: 20 MM KCL, 1 MM BACL2, 1 MM EDTA, 20 MM TRIS / pH: 7.6 / Details: 20 MM KCL, 1 MM BACL2, 1 MM EDTA, 20 MM TRIS
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: PLUNGE FREEZING

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Data collection

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Mar 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3077 nm / Nominal defocus min: 655 nm / Cs: 2 mm
Specimen holderTemperature: 85 K / Tilt angle max: 46 ° / Tilt angle min: 0 °
Image recordingElectron dose: 5 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 78
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionResolution: 7 Å / Resolution method: OTHER / Symmetry type: 2D CRYSTAL
RefinementHighest resolution: 7 Å
Refinement stepCycle: LAST / Highest resolution: 7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10340 0 2 0 10342

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