SAXSdb — 9pxn

▼

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

Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Thermostable Green Protein

synthetic construct

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–635 Chain B； UniProt 2–635 Chain C； UniProt 2–635 Chain D； UniProt 2–635	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.50 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 9PXN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5U6O Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel Deposited 2016-12-08	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain A 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain B 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain B 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain C 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain C 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain D 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain D 866–890（25 aa） Fragment：UNP residues 1-635,866-890	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
5U6P Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP Deposited 2016-12-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain A 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain B 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain B 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain C 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain C 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain D 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain D 866–890（25 aa） Fragment：UNP residues 1-635,866-890	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.51 Å
6UQF Human HCN1 channel in a hyperpolarized conformation Deposited 2019-10-19	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Chain A 866–890（25 aa） Chain B 1–635（635 aa） Chain B 866–890（25 aa） Chain C 1–635（635 aa） Chain C 866–890（25 aa） Chain D 1–635（635 aa） Chain D 866–890（25 aa）	Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 HG MERCURY (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
6UQG Human HCN1 channel Y289D mutant Deposited 2019-10-19	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Chain A 866–890（25 aa） Chain B 1–635（635 aa） Chain B 866–890（25 aa） Chain C 1–635（635 aa） Chain C 866–890（25 aa） Chain D 1–635（635 aa） Chain D 866–890（25 aa）	Mutation：Y289D Mutation：Y289D Mutation：Y289D Mutation：Y289D Mutation：Y289D Mutation：Y289D Mutation：Y289D Mutation：Y289D	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8T4M Closed human HCN1 F186C S264C bound to cAMP, reconstituted in LMNG + SPL Deposited 2023-06-09	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–890（890 aa） Chain B 1–890（890 aa） Chain C 1–890（890 aa） Chain D 1–890（890 aa）	Mutation：F186C S264C Mutation：F186C S264C Mutation：F186C S264C Mutation：F186C S264C	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
8T4Y Human HCN1 F186C S264C C309A bound to cAMP, reconstituted in LMNG + SPL Deposited 2023-06-12	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–890（890 aa） Chain B 1–890（890 aa） Chain C 1–890（890 aa） Chain D 1–890（890 aa）	Mutation：F186C, S264C, C309A Mutation：F186C, S264C, C309A Mutation：F186C, S264C, C309A Mutation：F186C, S264C, C309A	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
8T50 Open human HCN1 F186C S264C bound to cAMP, reconstituted in LMNG + SPL Deposited 2023-06-12	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–890（890 aa） Chain B 1–890（890 aa） Chain C 1–890（890 aa） Chain D 1–890（890 aa）	Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C Mutation：F186C, S264C	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8UC7 HCN1 complex with propofol Deposited 2023-09-25	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain A 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain B 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain B 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain C 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain C 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain D 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain D 866–890（25 aa） Fragment：UNP residues 1-635,866-890	Not recorded	PFL 2,6-BIS(1-METHYLETHYL)PHENOL × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8UC8 HCN1 nanodisc Deposited 2023-09-25	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain A 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain B 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain B 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain C 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain C 866–890（25 aa） Fragment：UNP residues 1-635,866-890 Chain D 1–635（635 aa） Fragment：UNP residues 1-635,866-890 Chain D 866–890（25 aa） Fragment：UNP residues 1-635,866-890	Not recorded	PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8Y60 Structural mechanism of human HCN1 hyperpolarization-activated channel inhibition by ivabradine Deposited 2024-02-01	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–890（890 aa） Chain B 1–890（890 aa） Chain C 1–890（890 aa） Chain D 1–890（890 aa）	Not recorded	CLR CHOLESTEROL × 4 VNZ Ivabradine × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9BC6 HCN1 M305L with propofol Deposited 2024-04-07	Different construct Different mutation/modification Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Chain A 866–890（25 aa） Chain B 1–635（635 aa） Chain B 866–890（25 aa） Chain C 1–635（635 aa） Chain C 866–890（25 aa） Chain D 1–635（635 aa） Chain D 866–890（25 aa）	Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L	PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PFL 2,6-BIS(1-METHYLETHYL)PHENOL × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9BC7 HCN1 M305L holo Deposited 2024-04-08	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–635（635 aa） Chain A 866–890（25 aa） Chain B 1–635（635 aa） Chain B 866–890（25 aa） Chain C 1–635（635 aa） Chain C 866–890（25 aa） Chain D 1–635（635 aa） Chain D 866–890（25 aa）	Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L Mutation：M305L	PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9R1T Structure of the human chimera HCN112 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP. Deposited 2025-04-28	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–401（401 aa） Chain B 1–401（401 aa） Chain C 1–401（401 aa） Chain D 1–401（401 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9R1U Structure of the human HCN1dC hyperpolarization-activated cyclic nucleotide-gated ion channel. Deposited 2025-04-28	Different construct Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–401（401 aa） Chain B 1–401（401 aa） Chain C 1–401（401 aa） Chain D 1–401（401 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
9R1V Structure of the human chimera HCN112 hyperpolarization-activated cyclic nucleotide-gated ion channel. Deposited 2025-04-28	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–401（401 aa） Chain B 1–401（401 aa） Chain C 1–401（401 aa） Chain D 1–401（401 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
9Z6T Human HCN1 in complex with cAMP in nanodisc Deposited 2025-11-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–635（634 aa） Chain B 2–635（634 aa） Chain C 2–635（634 aa） Chain D 2–635（634 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HCN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–645； UniProt 2–635 Author chain B； PDBConstruct 12–645； UniProt 2–635 Author chain C； PDBConstruct 12–645； UniProt 2–635 Author chain D； PDBConstruct 12–645； UniProt 2–635

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pxn
Deposition date deposition_date	2025-08-06
Structure title title	Human apo HCN1 nanodisc
Keywords keywords	ion channel, pacemaker channel, hyperpolarization-activated, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	41.38 Å
Radius of gyration Rg (electron density) rg_electron	41.04 Å
Forward intensity I(0) i0	672165000.00
Molecular weight molecular_weight	223230.0 kDa
Excluded volume excluded_volume	283430 Å³
Envelope volume envelope_volume	401400 Å³
Hydration-shell volume shell_volume	77687 Å³
Envelope diameter envelope_diameter	128.9 Å
Shell Rg shell_rg	49.48 Å
Envelope Rg envelope_rg	40.46 Å
Shape Rg shape_rg	41.00 Å
Total Rg total_rg	41.61 Å
Total atoms total_atoms	31460
Residues n_residues	1916
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	127.1 Å
Rg (real space) rg_real	41.14 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	6.7220e+08
I(0) uncertainty (real space) i0_real_error	1.0780e+07
Rg (reciprocal space) rg_reciprocal	41.38 Å
I(0) (reciprocal space) i0_reciprocal	672300000.0000
Solution quality estimate total_estimate	0.8900
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.5 Å
Skewness Skewness skewness	0.085
Kurtosis Kurtosis kurtosis	-0.470
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55690000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.909

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Description description	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Thermostable Green Protein
Molecular weight formula_weight	103035.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	31460

MDYKDDDDKGSEGGGKPNSSSNSRDDGNSVFPAKASATGAGPAAAEKRLGTPPGGGGAGAKEHGNSVCFKVDGGGGGGGGGGGGEEPAGGFEDAEGPRRQYGFMQRQFTSMLQPGVNKFSLRMFGSQKAVEKEQERVKTAGFWIIHPYSDFRFYWDLIMLIMMVGNLVIIPVGITFFTEQTTTPWIIFNVASDTVFLLDLIMNFRTGTVNEDSSEIILDPKVIKMNYLKSWFVVDFISSIPVDYIFLIVEKGMDSEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLASAVVRIFNLIGMMLLLCHWDGCLQFLVPLLQDFPPDCWVSLNEMVNDSWGKQYSYALFKAMSHMLCIGYGAQAPVSMSDLWITMLSMIVGATCYAMFVGHATALIQSLDSSRRQYQEKYKQVEQYMSFHKLPADMRQKIHDYYEHRYQGKIFDEENILNELNDPLREEIVNFNCRKLVATMPLFANADPNFVTAMLSKLRFEVFQPGDYIIREGAVGKKMYFIQHGVAGVITKSSKEMKLTDGSYFGEICLLTKGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLQKFQKDLNTGVFNNQENEILKQIVKHDREMVQAASNSGLNDIFEAQKIEWHELEVLFQGPTAAMSVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGHHHHHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Komagataella pastoris

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	236378

fit	/app/data/saxs_computation/px/9pxn/9pxn.fit
pddf	/app/data/pr_computation/px/9pxn/9pxn.pr.out
profile	/app/data/saxs_computation/px/9pxn/9pxn.dat

Human apo HCN1 nanodisc

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

Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1,Thermostable Green Protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)