SAXSdb — 5u6o

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

Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1

Homo sapiens

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 1–635 Chain A； UniProt 866–890 Chain B； UniProt 1–635 Chain B； UniProt 866–890 Chain C； UniProt 1–635 Chain C； UniProt 866–890 Chain D； UniProt 1–635 Chain D； UniProt 866–890	Fragment：UNP residues 1-635,866-890	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.50 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 5U6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5U6P Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP Deposited 2016-12-08	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 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 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 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）	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 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 × 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
9PXN Human apo HCN1 nanodisc Deposited 2025-08-06	Different construct Different mutation/modification 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	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 construct Different mutation/modification 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 1–635； UniProt 1–635 Author chain A； PDBConstruct 636–660； UniProt 866–890 Author chain B； PDBConstruct 1–635； UniProt 1–635 Author chain B； PDBConstruct 636–660； UniProt 866–890 Author chain C； PDBConstruct 1–635； UniProt 1–635 Author chain C； PDBConstruct 636–660； UniProt 866–890 Author chain D； PDBConstruct 1–635； UniProt 1–635 Author chain D； PDBConstruct 636–660； UniProt 866–890

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5u6o
Deposition date deposition_date	2016-12-08
Structure title title	Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel
Keywords keywords	pacemaker ion channel, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	39.95 Å
Radius of gyration Rg (electron density) rg_electron	39.24 Å
Forward intensity I(0) i0	590771000.00
Molecular weight molecular_weight	205000.0 kDa
Excluded volume excluded_volume	258290 Å³
Envelope volume envelope_volume	359130 Å³
Hydration-shell volume shell_volume	72387 Å³
Envelope diameter envelope_diameter	123.6 Å
Shell Rg shell_rg	47.98 Å
Envelope Rg envelope_rg	38.88 Å
Shape Rg shape_rg	39.30 Å
Total Rg total_rg	39.52 Å
Total atoms total_atoms	14480
Residues n_residues	1928
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

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

Maximum dimension Dmax dmax	122.0 Å
Rg (real space) rg_real	39.60 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	5.9080e+08
I(0) uncertainty (real space) i0_real_error	9.4120e+06
Rg (reciprocal space) rg_reciprocal	39.82 Å
I(0) (reciprocal space) i0_reciprocal	590900000.0000
Solution quality estimate total_estimate	0.8925
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.8 Å
Skewness Skewness skewness	0.084
Kurtosis Kurtosis kurtosis	-0.470
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51690000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.921

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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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	3.500 Å
Low-resolution limit resolution_low	124.800 Å
R factor r_factor	0.3117
R_work r_work	0.3117
R_free r_free	—

Resolution resolution	3.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	55870

Description description	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
Molecular weight formula_weight	74643.7 kDa
Source method src_method	man
Copy count entity_count	4

Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel

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

Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1

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)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14480

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

fit	/app/data/saxs_computation/u6/5u6o/5u6o.fit
pddf	/app/data/pr_computation/u6/5u6o/5u6o.pr.out
profile	/app/data/saxs_computation/u6/5u6o/5u6o.dat