← Back to search
9upf

Cryo-EM structure of human olfactory CNG channel in cAMP-bound open state

Method: ELECTRON MICROSCOPY Dmax: 124.0 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cyclic nucleotide-gated channel beta-1

Homo sapiens

UniProt Q14028

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–1251 Not recorded Cyclic nucleotide-gated channel alpha-2 × 2 （Q16280） Cyclic nucleotide-gated channel alpha-4 × 1 （Q8IV77） CA CALCIUM ION × 2 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.59 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9UPF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7RH9 Cryo-EM structure of human rod CNGA1/B1 channel in apo state Deposited 2021-07-16 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
7RHG Cryo-EM structure of human rod CNGA1/B1 channel in cAMP-bound state Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7RHH Cryo-EM structure of human rod CNGA1/B1 channel in cGMP-bound openI state Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
7RHI Cryo-EM structure of human rod CNGA1/B1 channel in cGMP-bound openII state Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
7RHJ Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-Diltiazem-blocked open state Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 4 5H0 (2R,3R)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
7RHK Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-Diltiazem-trapped closed state Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 4 5H0 (2R,3R)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
7RHL Cryo-EM structure of human rod Apo CNGA1/B1 channel with CLZ coiled coil Deposited 2021-07-17 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 454–1251（798 aa） Fragment：UNP residues 454-1251
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
8DGH NMR Structure of calmodulin bound to C-terminal site in the beta-subunit of cyclic nucleotide-gated channel Deposited 2022-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1128–1139（12 aa） Fragment：C-terminal site, residues 1128-1139
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 1；Pressure 1
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] Calmodulin, 1.2 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] Calmodulin, 1.2 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O | 100% D2O
Resolution not provided
8DGK NMR structure of calmodulin bound to N-terminal site in the beta-subunit of cyclic nucleotide-gated channel Deposited 2022-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 565–576（12 aa） Fragment：N-terminal site, residues 565-576
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 1；Pressure 1
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O | 100% D2O
NMR sample composition 0.5 mM [U-10% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O | 100% D2O
Resolution not provided
9UPG Cryo-EM structure of human olfactory CNGA2/A4/B1 in CaM-bound closed state Deposited 2025-04-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–1251（1251 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CNGB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–1251； UniProt 1–1251

Cyclic nucleotide-gated channel alpha-2

Homo sapiens

UniProt Q16280

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–664 Chain C； UniProt 1–664 Not recorded Cyclic nucleotide-gated channel beta-1 × 1 （Q14028） Cyclic nucleotide-gated channel alpha-4 × 1 （Q8IV77） CA CALCIUM ION × 2 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.59 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9UPF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6FIZ Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+ Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 339–344（6 aa）
Chain B 339–344（6 aa）
Chain C 339–344（6 aa）
Chain D 339–344（6 aa）
Not recorded GLY GLYCINE × 10 K POTASSIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；40-44% MPD 100 mM MES pH 6.5 25mM Glycine
Resolution 2.63 Å R-free 0.269
6FIZ Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+ Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 339–344（6 aa）
Chain F 339–344（6 aa）
Chain G 339–344（6 aa）
Chain H 339–344（6 aa）
Not recorded GLY GLYCINE × 12 K POTASSIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；40-44% MPD 100 mM MES pH 6.5 25mM Glycine
Resolution 2.63 Å R-free 0.269
6FIZ Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+ Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 339–344（6 aa）
Chain J 339–344（6 aa）
Chain K 339–344（6 aa）
Chain L 339–344（6 aa）
Not recorded GLY GLYCINE × 17 K POTASSIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；40-44% MPD 100 mM MES pH 6.5 25mM Glycine
Resolution 2.63 Å R-free 0.269
6FIZ Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+ Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain M 339–344（6 aa）
Chain N 339–344（6 aa）
Chain O 339–344（6 aa）
Chain P 339–344（6 aa）
Not recorded GLY GLYCINE × 21 K POTASSIUM ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；40-44% MPD 100 mM MES pH 6.5 25mM Glycine
Resolution 2.63 Å R-free 0.269
9UPG Cryo-EM structure of human olfactory CNGA2/A4/B1 in CaM-bound closed state Deposited 2025-04-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–664（664 aa）
Chain C 1–664（664 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CNGA2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–664； UniProt 1–664 Author chain C； PDBConstruct 1–664； UniProt 1–664

Cyclic nucleotide-gated channel alpha-4

Homo sapiens

UniProt Q8IV77

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–575 Not recorded Cyclic nucleotide-gated channel beta-1 × 1 （Q14028） Cyclic nucleotide-gated channel alpha-2 × 2 （Q16280） CA CALCIUM ION × 2 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.59 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9UPF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9UPG Cryo-EM structure of human olfactory CNGA2/A4/B1 in CaM-bound closed state Deposited 2025-04-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–575（575 aa）
Not recorded CA CALCIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CNGA4_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–575； UniProt 1–575

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9upf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9upf
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9upf
Deposition date deposition_date2025-04-28
Structure title titleCryo-EM structure of human olfactory CNG channel in cAMP-bound open state
Keywords keywordsIon Channels, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.60 Å
Radius of gyration Rg (electron density) rg_electron39.90 Å
Forward intensity I(0) i0567905000.00
Molecular weight molecular_weight206810.0 kDa
Excluded volume excluded_volume263570 ų
Envelope volume envelope_volume368320 ų
Hydration-shell volume shell_volume74350 ų
Envelope diameter envelope_diameter125.6 Å
Shell Rg shell_rg48.05 Å
Envelope Rg envelope_rg38.83 Å
Shape Rg shape_rg39.89 Å
Total Rg total_rg40.40 Å
Total atoms total_atoms14581
Residues n_residues1774
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax124.0 Å
Rg (real space) rg_real40.35 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real5.6790e+08
I(0) uncertainty (real space) i0_real_error9.0480e+06
Rg (reciprocal space) rg_reciprocal40.60 Å
I(0) (reciprocal space) i0_reciprocal568000000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.0 Å
Skewness Skewness skewness0.054
Kurtosis Kurtosis kurtosis-0.495
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49290000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.935
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▶

8. Citations (1)

▶

9. Files and Curves (10)