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- EMDB-21651: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21651
TitleStructure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
Map datacGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
Sample
  • Complex: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
    • Protein or peptide: Cyclic nucleotide-gated cation channel
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: SODIUM ION
KeywordsIon channel / vision / olfaction / phototransduction / blindness / cyclic nucleotide-gated channel / lipid nanodiscs / MEMBRANE PROTEIN
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 / protein-containing complex binding / positive regulation of gene expression / 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
Cyclic nucleotide-gated channel
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsZheng X / Fu Z
Funding support United States, China, 6 items
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, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wel
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21651.png

Downloads & links

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Map

FileDownload / File: emd_21651.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 296 pix.
= 313.76 Å		1.06 Å/pix.
x 296 pix.
= 313.76 Å		1.06 Å/pix.
x 296 pix.
= 313.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.21 / Movie #1: 0.21
Minimum - Maximum-2.3844783 - 3.5539935
Average (Standard dev.)0.0008006836 (±0.07052116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 313.75998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z313.760313.760313.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS296296296
D min/max/mean-2.3843.5540.001

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Supplemental data

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Sample components

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Entire : Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted ...

EntireName: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
Components
  • Complex: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
    • Protein or peptide: Cyclic nucleotide-gated cation channel
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: SODIUM ION

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Supramolecule #1: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted ...

SupramoleculeName: Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Cyclic nucleotide-gated cation channel

MacromoleculeName: Cyclic nucleotide-gated cation channel / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 83.914523 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTAEPAPDP TNPSTSGLAP TTNGIGSPPP TASAATKFSI LTKFLRRKNQ VHTTTAQQNE FMQKYMPNGN SNAVQPAATG GQPASSDGG SAIEVPPPKE SYAVRIRKYL ANYTQDPSTD NFYYWTCVVT VAYIYNLLFV IARQVFNDLI GPSSQSLCRF Y NGTLNSTT ...String:
MSTAEPAPDP TNPSTSGLAP TTNGIGSPPP TASAATKFSI LTKFLRRKNQ VHTTTAQQNE FMQKYMPNGN SNAVQPAATG GQPASSDGG SAIEVPPPKE SYAVRIRKYL ANYTQDPSTD NFYYWTCVVT VAYIYNLLFV IARQVFNDLI GPSSQSLCRF Y NGTLNSTT QVECTYNMLT NMKEMPTYSQ YPDLGWSKYW HFRMLWVFFD LLMDCVYLID TFLNYRMGYM DQGLVVREAE KV TKAYWQS KQYRIDGISL IPLDYILGWP IPYINWRGLP ILRLNRLIRY KRVRNCLERT ETRSSMPNAF RVVVVVWYIV III HWNACL YFWISEWIGL GTDAWVYGHL NKQSLPDDIT DTLLRRYVYS FYWSTLILTT IGEVPSPVRN IEYAFVTLDL MCGV LIVAT IAGNVGSMIS NMSAARTEFQ NKMDGIKQYM ELRKVSKQLE IRVIKWFDYL WTNKQSLSDQ QVLKVLPDKL QAEIA MQVH FETLRKVRIF QDCEAGLLAE LVLKLQLQVF SPGDFICKKG DIGREMYIVK RGRLQVVDDD GKKVFVTLQE GSVFGE LSI LNIAGSKNGN RRTANVRSVG YTDLFVLSKT DLWNALREYP DARKLLLAKG REILKKDNLL DENAPEEQKT VEEIAEH LN NAVKVLQTRM ARLIVEHSST EGKLMKRIEM LEKHLSRYKA LARRQKTMHG VSIDGGDIST DGVDERVRPP RLRQTKTI D LPTGTESESL LK

UniProtKB: Cyclic nucleotide-gated channel

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Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 28 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #3: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1877870
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5h3o

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 445131
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

5h3o


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6wel:
Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs

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