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- EMDB-28603: Cryo-EM structure of cGMP bound human CNGA3/CNGB3 channel in GDN,... -

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Basic information

Entry
Database: EMDB / ID: EMD-28603
TitleCryo-EM structure of cGMP bound human CNGA3/CNGB3 channel in GDN, transition state 1
Map data
Sample
  • Complex: human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3 in complex with cGMP in GDN
    • Protein or peptide: Cyclic nucleotide-gated cation channel alpha-3
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
KeywordsHeterotetramer / ligand-bound / MEMBRANE PROTEIN
Function / homology
Function and homology information


inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / sodium channel activity / myosin binding / response to magnesium ion / monoatomic cation transmembrane transport / monoatomic cation transport ...inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / axon initial segment / sodium channel activity / myosin binding / response to magnesium ion / monoatomic cation transmembrane transport / monoatomic cation transport / transmembrane transporter complex / cGMP binding / glial cell projection / ligand-gated monoatomic ion channel activity / photoreceptor outer segment / response to cAMP / visual perception / calcium channel activity / perikaryon / cadherin binding / dendrite / protein-containing complex binding / signal transduction / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / 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-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / : / 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 alpha-3 / Cyclic nucleotide-gated channel beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsHu Z / Zheng X / Yang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Nat Commun / Year: 2023
Title: Conformational trajectory of allosteric gating of the human cone photoreceptor cyclic nucleotide-gated channel.
Authors: Zhengshan Hu / Xiangdong Zheng / Jian Yang /
Abstract: Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide- ...Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide-binding domain (CNBD) to open a gate located 50-60 Å away in the central cavity. Structures of closed and open vertebrate CNG channels have been solved, but the conformational landscape of this allosteric gating remains to be elucidated and enriched. Here, we report structures of the cGMP-activated human cone photoreceptor CNGA3/CNGB3 channel in closed, intermediate, pre-open and open states in detergent or lipid nanodisc, all with fully bound cGMP. The pre-open and open states are obtained only in the lipid nanodisc, suggesting a critical role of lipids in tuning the energetic landscape of CNGA3/CNGB3 activation. The different states exhibit subunit-unique, incremental and distinct conformational rearrangements that originate in the CNBD, propagate through the gating ring to the transmembrane domain, and gradually open the S6 cavity gate. Our work illustrates a spatial conformational-change wave of allosteric gating of a vertebrate CNG channel by its natural ligand and provides an expanded framework for studying CNG properties and channelopathy.
History
DepositionOct 18, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28603.png

Downloads & links

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Map

FileDownload / File: emd_28603.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 296 pix.
= 313.168 Å		1.06 Å/pix.
x 296 pix.
= 313.168 Å		1.06 Å/pix.
x 296 pix.
= 313.168 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.445
Minimum - Maximum-2.608228 - 3.817547
Average (Standard dev.)0.0033709684 (±0.071547724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 313.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28603_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28603_half_map_2.map
Projections & Slices
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Sample components

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Entire : human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3...

EntireName: human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3 in complex with cGMP in GDN
Components
  • Complex: human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3 in complex with cGMP in GDN
    • Protein or peptide: Cyclic nucleotide-gated cation channel alpha-3
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE

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Supramolecule #1: human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3...

SupramoleculeName: human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3 in complex with cGMP in GDN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cyclic nucleotide-gated cation channel alpha-3

MacromoleculeName: Cyclic nucleotide-gated cation channel alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.93793 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAKINTQYSH PSRTHLKVKT SDRDLNRAEN GLSRAHSSSE ETSSVLQPGI AMETRGLADS GQGSFTGQGI ARLSRLIFLL RRWAARHVH HQDQGPDSFP DRFRGAELKE VSSQESNAQA NVGSQEPADR GRSAWPLAKC NTNTSNNTEE EKKTKKKDAI V VDPSSNLY ...String:
MAKINTQYSH PSRTHLKVKT SDRDLNRAEN GLSRAHSSSE ETSSVLQPGI AMETRGLADS GQGSFTGQGI ARLSRLIFLL RRWAARHVH HQDQGPDSFP DRFRGAELKE VSSQESNAQA NVGSQEPADR GRSAWPLAKC NTNTSNNTEE EKKTKKKDAI V VDPSSNLY YRWLTAIALP VFYNWYLLIC RACFDELQSE YLMLWLVLDY SADVLYVLDV LVRARTGFLE QGLMVSDTNR LW QHYKTTT QFKLDVLSLV PTDLAYLKVG TNYPEVRFNR LLKFSRLFEF FDRTETRTNY PNMFRIGNLV LYILIIIHWN ACI YFAISK FIGFGTDSWV YPNISIPEHG RLSRKYIYSL YWSTLTLTTI GETPPPVKDE EYLFVVVDFL VGVLIFATIV GNVG SMISN MNASRAEFQA KIDSIKQYMQ FRKVTKDLET RVIRWFDYLW ANKKTVDEKE VLKSLPDKLK AEIAINVHLD TLKKV RIFQ DCEAGLLVEL VLKLRPTVFS PGDYICKKGD IGKEMYIINE GKLAVVADDG VTQFVVLSDG SYFGEISILN IKGSKS GNR RTANIRSIGY SDLFCLSKDD LMEALTEYPE AKKALEEKGR QILMKDNLID EELARAGADP KDLEEKVEQL GSSLDTL QT RFARLLAEYN ATQMKMKQRL SQLESQVKGG GDKPLADGEV PGDATKTEDK QQ

UniProtKB: Cyclic nucleotide-gated channel alpha-3

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Macromolecule #2: Cyclic nucleotide-gated cation channel beta-3

MacromoleculeName: Cyclic nucleotide-gated cation channel beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.289492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFKSLTKVNK VKPIGENNEN EQSSRRNEEG SHPSNQSQQT TAQEENKGEE KSLKTKSTPV TSEEPHTNIQ DKLSKKNSSG DLTTNPDPQ NAAEPTGTVP EQKEMDPGKE GPNSPQNKPP AAPVINEYAD AQLHNLVKRM RQRTALYKKK LVEGDLSSPE A SPQTAKPT ...String:
MFKSLTKVNK VKPIGENNEN EQSSRRNEEG SHPSNQSQQT TAQEENKGEE KSLKTKSTPV TSEEPHTNIQ DKLSKKNSSG DLTTNPDPQ NAAEPTGTVP EQKEMDPGKE GPNSPQNKPP AAPVINEYAD AQLHNLVKRM RQRTALYKKK LVEGDLSSPE A SPQTAKPT AVPPVKESDD KPTEHYYRLL WFKVKKMPLT EYLKRIKLPN SIDSYTDRLY LLWLLLVTLA YNWNCCFIPL RL VFPYQTA DNIHYWLIAD IICDIIYLYD MLFIQPRLQF VRGGDIIVDS NELRKHYRTS TKFQLDVASI IPFDICYLFF GFN PMFRAN RMLKYTSFFE FNHHLESIMD KAYIYRVIRT TGYLLFILHI NACVYYWASN YEGIGTTRWV YDGEGNEYLR CYYW AVRTL ITIGGLPEPQ TLFEIVFQLL NFFSGVFVFS SLIGQMRDVI GAATANQNYF RACMDDTIAY MNNYSIPKLV QKRVR TWYE YTWDSQRMLD ESDLLKTLPT TVQLALAIDV NFSIISKVDL FKGCDTQMIY DMLLRLKSVL YLPGDFVCKK GEIGKE MYI IKHGEVQVLG GPDGTKVLVT LKAGSVFGEI SLLAAGGGNR RTANVVAHGF ANLLTLDKKT LQEILVHYPD SERILMK KA RVLLKQKAKT AEATPPRKDL ALLFPPKEET PKLFKTLLGG TGKASLARLL KLKREQAAQK KENSEGGEEE GKENEDKQ K ENEDKQKENE DKGKENEDKD KGREPEEKPL DRPECTASPI AVEEEPHSVR RTVLPRGTSR QSLIISMAPS AEGGEEVLT IEVKEKAKQ

UniProtKB: Cyclic nucleotide-gated channel beta-3

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: CYCLIC GUANOSINE MONOPHOSPHATE

MacromoleculeName: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: PCG
Molecular weightTheoretical: 345.205 Da
Chemical component information

ChemComp-PCG:
CYCLIC GUANOSINE MONOPHOSPHATE

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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: 8.58
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131492
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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