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- EMDB-64394: Cryo-EM structure of human olfactory CNG channel in cAMP-bound op... -

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Basic information

Entry
Database: EMDB / ID: EMD-64394
TitleCryo-EM structure of human olfactory CNG channel in cAMP-bound open state
Map data
Sample
  • Complex: human olfactory CNG channels
    • Protein or peptide: Cyclic nucleotide-gated channel beta-1
    • Protein or peptide: Cyclic nucleotide-gated channel alpha-2
    • Protein or peptide: Cyclic nucleotide-gated channel alpha-4
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
KeywordsIon Channels / MEMBRANE PROTEIN
Function / homology
Function and homology information


olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / response to odorant / intracellular cyclic nucleotide activated cation channel complex / protein localization to organelle / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment ...olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / response to odorant / intracellular cyclic nucleotide activated cation channel complex / protein localization to organelle / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / VxPx cargo-targeting to cilium / detection of light stimulus involved in visual perception / Golgi-associated vesicle membrane / transmembrane transporter complex / photoreceptor cell maintenance / retina homeostasis / ligand-gated monoatomic ion channel activity / ciliary membrane / sodium ion transport / sodium channel activity / monoatomic cation transmembrane transport / cGMP binding / monoatomic cation transport / membrane depolarization / phototransduction / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / cAMP binding / visual perception / potassium ion transport / calcium channel activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / terminal bouton / calcium ion transport / sensory perception of smell / Inactivation, recovery and regulation of the phototransduction cascade / calmodulin binding / G protein-coupled receptor signaling pathway / positive regulation of gene expression / protein-containing complex binding / 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 beta-1 / Cyclic nucleotide-gated channel alpha-2 / Cyclic nucleotide-gated channel alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsXue J / Jiang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structural mechanisms underlying assembly, gating, and calmodulin inhibition of olfactory CNG channels
Authors: Xue J / Jiang Y
History
DepositionApr 28, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64394.png

Downloads & links

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Map

FileDownload / File: emd_64394.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 450 pix.
= 332.1 Å		0.74 Å/pix.
x 450 pix.
= 332.1 Å		0.74 Å/pix.
x 450 pix.
= 332.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.738 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2060324 - 1.4956697
Average (Standard dev.)0.002677795 (±0.04196505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 332.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CNBD focused map

Fileemd_64394_additional_1.map
AnnotationCNBD focused map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: TM focused map

Fileemd_64394_additional_2.map
AnnotationTM focused map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64394_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64394_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human olfactory CNG channels

EntireName: human olfactory CNG channels
Components
  • Complex: human olfactory CNG channels
    • Protein or peptide: Cyclic nucleotide-gated channel beta-1
    • Protein or peptide: Cyclic nucleotide-gated channel alpha-2
    • Protein or peptide: Cyclic nucleotide-gated channel alpha-4
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

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Supramolecule #1: human olfactory CNG channels

SupramoleculeName: human olfactory CNG channels / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cyclic nucleotide-gated channel beta-1

MacromoleculeName: Cyclic nucleotide-gated channel beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.831812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGWVQRVLP QPPGTPRKTK MQEEEEVEPE PEMEAEVEPE PNPEEAETES ESMPPEESFK EEEVAVADPS PQETKEAALT STISLRAQG AEISEMNSPS RRVLTWLMKG VEKVIPQPVH SITEDPAQIL GHGSTGDTGC TDEPNEALEA QDTRPGLRLL L WLEQNLER ...String:
MLGWVQRVLP QPPGTPRKTK MQEEEEVEPE PEMEAEVEPE PNPEEAETES ESMPPEESFK EEEVAVADPS PQETKEAALT STISLRAQG AEISEMNSPS RRVLTWLMKG VEKVIPQPVH SITEDPAQIL GHGSTGDTGC TDEPNEALEA QDTRPGLRLL L WLEQNLER VLPQPPKSSE VWRDEPAVAT GAASDPAPPG RPQEMGPKLQ ARETPSLPTP IPLQPKEEPK EAPAPEPQPG SQ AQTSSLP PTRDPARLVA WVLHRLEMAL PQPVLHGKIG EQEPDSPGIC DVQTISILPG GQVEPDLVLE EVEPPWEDAH QDV STSPQG TEVVPAYEEE NKAVEKMPRE LSRIEEEKED EEEEEEEEEE EEEEEVTEVL LDSCVVSQVG VGQSEEDGTR PQST SDQKL WEEVGEEAKK EAEEKAKEEA EEVAEEEAEK EPQDWAETKE EPEAEAEAAS SGVPATKQHP EVQVEDTDAD SCPLM AEEN PPSTVLPPPS PAKSDTLIVP SSASGTHRKK LPSEDDEAEE LKALSPAESP VVAWSDPTTP KDTDGQDRAA STASTN SAI INDRLQELVK LFKERTEKVK EKLIDPDVTS DEESPKPSPA KKAPEPAPDT KPAEAEPVEE EHYCDMLCCK FKHRPWK KY QFPQSIDPLT NLMYVLWLFF VVMAWNWNCW LIPVRWAFPY QTPDNIHHWL LMDYLCDLIY FLDITVFQTR LQFVRGGD I ITDKKDMRNN YLKSRRFKMD LLSLLPLDFL YLKVGVNPLL RLPRCLKYMA FFEFNSRLES ILSKAYVYRV IRTTAYLLY SLHLNSCLYY WASAYQGLGS THWVYDGVGN SYIRCYYFAV KTLITIGGLP DPKTLFEIVF QLLNYFTGVF AFSVMIGQMR DVVGAATAG QTYYRSCMDS TVKYMNFYKI PKSVQNRVKT WYEYTWHSQG MLDESELMVQ LPDKMRLDLA IDVNYNIVSK V ALFQGCDR QMIFDMLKRL RSVVYLPNDY VCKKGEIGRE MYIIQAGQVQ VLGGPDGKSV LVTLKAGSVF GEISLLAVGG GN RRTANVV AHGFTNLFIL DKKDLNEILV HYPESQKLLR KKARRMLRSN NKPKEEKSVL ILPPRAGTPK LFNAALAMTG KMG GKGAKG GKLAHLRARL KELAALEAAA KQQELVEQAK SSQDVKGEEG SAAPDQHTHP KEAATDPPAP RTPPEPPGSP PSSP PPASL GRPEGEEEGP AEPEEHSVRI CMSPGPEPGE QILSVKMPEE REEKAE

UniProtKB: Cyclic nucleotide-gated channel beta-1

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Macromolecule #2: Cyclic nucleotide-gated channel alpha-2

MacromoleculeName: Cyclic nucleotide-gated channel alpha-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.144062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTEKTNGVKS SPANNHNHHA PPAIKANGKD DHRTSSRPHS AADDDTSSEL QRLADVDAPQ QGRSGFRRIV RLVGIIREWA NKNFREEEP RPDSFLERFR GPELQTVTTQ EGDGKGDKDG EDKGTKKKFE LFVLDPAGDW YYCWLFVIAM PVLYNWCLLV A RACFSDLQ ...String:
MTEKTNGVKS SPANNHNHHA PPAIKANGKD DHRTSSRPHS AADDDTSSEL QRLADVDAPQ QGRSGFRRIV RLVGIIREWA NKNFREEEP RPDSFLERFR GPELQTVTTQ EGDGKGDKDG EDKGTKKKFE LFVLDPAGDW YYCWLFVIAM PVLYNWCLLV A RACFSDLQ KGYYLVWLVL DYVSDVVYIA DLFIRLRTGF LEQGLLVKDT KKLRDNYIHT LQFKLDVASI IPTDLIYFAV DI HSPEVRF NRLLHFARMF EFFDRTETRT NYPNIFRISN LVLYILVIIH WNACIYYAIS KSIGFGVDTW VYPNITDPEY GYL AREYIY CLYWSTLTLT TIGETPPPVK DEEYLFVIFD FLIGVLIFAT IVGNVGSMIS NMNATRAEFQ AKIDAVKHYM QFRK VSKGM EAKVIRWFDY LWTNKKTVDE REILKNLPAK LRAEIAINVH LSTLKKVRIF HDCEAGLLVE LVLKLRPQVF SPGDY ICRK GDIGKEMYII KEGKLAVVAD DGVTQYALLS AGSCFGEISI LNIKGSKMGN RRTANIRSLG YSDLFCLSKD DLMEAV TEY PDAKKVLEER GREILMKEGL LDENEVATSM EVDVQEKLGQ LETNMETLYT RFGRLLAEYT GAQQKLKQRI TVLETKM KQ NNEDDYLSDG MNSPELAAAD EP

UniProtKB: Cyclic nucleotide-gated channel alpha-2

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Macromolecule #3: Cyclic nucleotide-gated channel alpha-4

MacromoleculeName: Cyclic nucleotide-gated channel alpha-4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.069656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQDTKVKTT ESSPPAPSKA RKLLPVLDPS GDYYYWWLNT MVFPVMYNLI ILVCRACFPD LQHGYLVAWL VLDYTSDLLY LLDMVVRFH TGFLEQGILV VDKGRISSRY VRTWSFFLDL ASLMPTDVVY VRLGPHTPTL RLNRFLRAPR LFEAFDRTET R TAYPNAFR ...String:
MSQDTKVKTT ESSPPAPSKA RKLLPVLDPS GDYYYWWLNT MVFPVMYNLI ILVCRACFPD LQHGYLVAWL VLDYTSDLLY LLDMVVRFH TGFLEQGILV VDKGRISSRY VRTWSFFLDL ASLMPTDVVY VRLGPHTPTL RLNRFLRAPR LFEAFDRTET R TAYPNAFR IAKLMLYIFV VIHWNSCLYF ALSRYLGFGR DAWVYPDPAQ PGFERLRRQY LYSFYFSTLI LTTVGDTPPP AR EEEYLFM VGDFLLAVMG FATIMGSMSS VIYNMNTADA AFYPDHALVK KYMKLQHVNR KLERRVIDWY QHLQINKKMT NEV AILQHL PERLRAEVAV SVHLSTLSRV QIFQNCEASL LEELVLKLQP QTYSPGEYVC RKGDIGQEMY IIREGQLAVV ADDG ITQYA VLGAGLYFGE ISIINIKGNM SGNRRTANIK SLGYSDLFCL SKEDLREVLS EYPQAQTIME EKGREILLKM NKLDV NAEA AEIALQEATE SRLRGLDQQL DDLQTKFARL LAELESSALK IAYRIERLEW QTREWPMPED LAEADDEGEP EEGTSK DEE GRASQEGPPG PE

UniProtKB: Cyclic nucleotide-gated channel alpha-4

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

MacromoleculeName: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: CMP
Molecular weightTheoretical: 329.206 Da
Chemical component information

ChemComp-CMP:
ADENOSINE-3',5'-CYCLIC-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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPHERA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43707
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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