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- PDB-6wej: Structure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs -

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Basic information

Entry
Database: PDB / ID: 6wej
TitleStructure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs
ComponentsCyclic nucleotide-gated cation channel
KeywordsMEMBRANE PROTEIN / Ion channel / vision / olfaction / phototransduction / blindness / lipid nanodiscs
Function / homology
Function and homology information


detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / ciliary inversin compartment / thermosensory behavior / positive regulation of growth rate / olfactory behavior / intracellular cyclic nucleotide activated cation channel complex ...detection of carbon dioxide / detection of chemical stimulus involved in sensory perception / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / VxPx cargo-targeting to cilium / ciliary inversin compartment / thermosensory behavior / positive regulation of growth rate / olfactory behavior / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / aerotaxis / chemosensory behavior / multicellular organismal reproductive process / intracellularly cAMP-activated cation channel activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / cation channel complex / response to oxygen levels / thermotaxis / non-motile cilium / regulation of neuron differentiation / regulation of axon extension / negative regulation of cGMP-mediated signaling / monoatomic cation transmembrane transport / phototransduction / cGMP binding / voltage-gated potassium channel activity / response to hyperoxia / neuron projection morphogenesis / calcium-mediated signaling / chemotaxis / dendrite / positive regulation of gene expression / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / 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
Chem-CPL / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Cyclic nucleotide-gated channel
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZheng, X. / Fu, Z. / Su, D. / Zhang, Y. / Li, M. / Pan, Y. / Li, H. / Li, S. / Grassucci, R.A. / Ren, Z. ...Zheng, X. / Fu, Z. / Su, D. / Zhang, Y. / Li, M. / Pan, Y. / Li, H. / Li, S. / Grassucci, R.A. / Ren, Z. / Hu, Z. / Li, X. / Zhou, M. / Li, G. / Frank, J. / Yang, J.
Funding support United States, China, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)RO1EY027800 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM085234 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM055440 United States
National Natural Science Foundation of China (NSFC)21625302 China
National Natural Science Foundation of China (NSFC)21573217 China
National Natural Science Foundation of China (NSFC)31700647 China
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel.
Authors: Xiangdong Zheng / Ziao Fu / Deyuan Su / Yuebin Zhang / Minghui Li / Yaping Pan / Huan Li / Shufang Li / Robert A Grassucci / Zhenning Ren / Zhengshan Hu / Xueming Li / Ming Zhou / Guohui Li ...Authors: Xiangdong Zheng / Ziao Fu / Deyuan Su / Yuebin Zhang / Minghui Li / Yaping Pan / Huan Li / Shufang Li / Robert A Grassucci / Zhenning Ren / Zhengshan Hu / Xueming Li / Ming Zhou / Guohui Li / Joachim Frank / Jian Yang /
Abstract: Cyclic nucleotide-gated (CNG) channels convert cyclic nucleotide (CN) binding and unbinding into electrical signals in sensory receptors and neurons. The molecular conformational changes underpinning ...Cyclic nucleotide-gated (CNG) channels convert cyclic nucleotide (CN) binding and unbinding into electrical signals in sensory receptors and neurons. The molecular conformational changes underpinning ligand activation are largely undefined. We report both closed- and open-state atomic cryo-EM structures of a full-length Caenorhabditis elegans cyclic GMP-activated channel TAX-4, reconstituted in lipid nanodiscs. These structures, together with computational and functional analyses and a mutant channel structure, reveal a double-barrier hydrophobic gate formed by two S6 amino acids in the central cavity. cGMP binding produces global conformational changes that open the cavity gate located ~52 Å away but do not alter the structure of the selectivity filter-the commonly presumed activation gate. Our work provides mechanistic insights into the allosteric gating and regulation of CN-gated and nucleotide-modulated channels and CNG channel-related channelopathies.
History
DepositionApr 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _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

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Structure visualization

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Assembly

Deposited unit
A: Cyclic nucleotide-gated cation channel
B: Cyclic nucleotide-gated cation channel
C: Cyclic nucleotide-gated cation channel
D: Cyclic nucleotide-gated cation channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,46437
Polymers335,9624
Non-polymers22,50233
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area41540 Å2
ΔGint-193 kcal/mol
Surface area97830 Å2

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Components

#1: Protein
Cyclic nucleotide-gated cation channel / Abnormal chemotaxis protein 4


Mass: 83990.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tax-4, ZC84.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03611
#2: Chemical...
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H52O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 66.03 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 801931
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163525 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5H3O

5h3o


Accession code: 5H3O / Source name: PDB / Type: experimental model

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