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- PDB-5u6o: Structure of the human HCN1 hyperpolarization-activated cyclic nu... -

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Basic information

Entry
Database: PDB / ID: 5u6o
TitleStructure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel
ComponentsPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
KeywordsTRANSPORT PROTEIN / pacemaker ion channel
Function / homology
Function and homology information


intracellular cAMP-activated cation channel activity involved in regulation of presynaptic membrane potential / HCN channels / general adaptation syndrome, behavioral process / HCN channel complex / retinal cone cell development / intracellularly cAMP-activated cation channel activity / regulation of membrane depolarization / apical protein localization / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity ...intracellular cAMP-activated cation channel activity involved in regulation of presynaptic membrane potential / HCN channels / general adaptation syndrome, behavioral process / HCN channel complex / retinal cone cell development / intracellularly cAMP-activated cation channel activity / regulation of membrane depolarization / apical protein localization / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / voltage-gated potassium channel activity / potassium channel activity / neuronal action potential / sodium ion transmembrane transport / cAMP binding / presynaptic active zone membrane / cellular response to cAMP / potassium ion transmembrane transport / regulation of membrane potential / postsynaptic membrane / protein homotetramerization / axon / glutamatergic synapse / dendrite / identical protein binding / plasma membrane
Similarity search - Function
Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 ...Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLee, C.-H. / MacKinnon, R.
CitationJournal: Cell / Year: 2017
Title: Structures of the Human HCN1 Hyperpolarization-Activated Channel.
Authors: Chia-Hsueh Lee / Roderick MacKinnon /
Abstract: Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels underlie the control of rhythmic activity in cardiac and neuronal pacemaker cells. In HCN, the polarity of voltage dependence is ...Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels underlie the control of rhythmic activity in cardiac and neuronal pacemaker cells. In HCN, the polarity of voltage dependence is uniquely reversed. Intracellular cyclic adenosine monophosphate (cAMP) levels tune the voltage response, enabling sympathetic nerve stimulation to increase the heart rate. We present cryo-electron microscopy structures of the human HCN channel in the absence and presence of cAMP at 3.5 Å resolution. HCN channels contain a K channel selectivity filter-forming sequence from which the amino acids create a unique structure that explains Na and K permeability. The voltage sensor adopts a depolarized conformation, and the pore is closed. An S4 helix of unprecedented length extends into the cytoplasm, contacts the C-linker, and twists the inner helical gate shut. cAMP binding rotates cytoplasmic domains to favor opening of the inner helical gate. These structures advance understanding of ion selectivity, reversed polarity gating, and cAMP regulation in HCN channels.
History
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

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Assembly

Deposited unit
A: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
B: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
C: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
D: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1


Theoretical massNumber of molelcules
Total (without water)298,5754
Polymers298,5754
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 94 - 586 / Label seq-ID: 94 - 586

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.001246, 0.999999, 0.000332), (-0.999999, 0.001246, 0.000723), (0.000723, -0.000332, 1)-0.09105, 124.71944, -0.01601
3given(-0.999999, 0.00131, 0.000614), (-0.00131, -0.999999, 0.000725), (0.000615, 0.000724, 1)124.73636, 124.87591, -0.0701
4given(0.000198, -1, 0.000119), (1, 0.000198, -0.000115), (0.000115, 0.000119, 1)124.81739, -0.01223, -0.01129

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Components

#1: Protein
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 / Brain cyclic nucleotide-gated channel 1 / BCNG-1


Mass: 74643.734 Da / Num. of mol.: 4 / Fragment: UNP residues 1-635,866-890
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCN1, BCNG1 / Production host: Homo sapiens (human) / References: UniProt: O60741

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pEG_BacMam
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 1.26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55870 / Symmetry type: POINT
RefinementResolution: 3.5→124.8 Å / Cor.coef. Fo:Fc: 0.89 / SU B: 26.745 / SU ML: 0.409 / ESU R: 0.768
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3117 --
obs0.3117 87152 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 242.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.01 Å2-0.01 Å2
2--0.21 Å2-0.01 Å2
3----0.43 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01914840
ELECTRON MICROSCOPYr_bond_other_d0.0020.0213364
ELECTRON MICROSCOPYr_angle_refined_deg1.2071.94320184
ELECTRON MICROSCOPYr_angle_other_deg0.891330352
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.58651916
ELECTRON MICROSCOPYr_dihedral_angle_2_deg23.38622.808584
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.112152160
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.8131572
ELECTRON MICROSCOPYr_chiral_restr0.0730.22268
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0217128
ELECTRON MICROSCOPYr_gen_planes_other0.0010.023696
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.38125.7057700
ELECTRON MICROSCOPYr_mcbond_other8.37825.7047699
ELECTRON MICROSCOPYr_mcangle_it13.17238.5719604
ELECTRON MICROSCOPYr_mcangle_other13.17138.5739605
ELECTRON MICROSCOPYr_scbond_it10.71426.0547140
ELECTRON MICROSCOPYr_scbond_other10.71326.0537139
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other18.29738.75310580
ELECTRON MICROSCOPYr_long_range_B_refined22.39929774
ELECTRON MICROSCOPYr_long_range_B_other22.39829775
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6961 / Refine-ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A1.05
B0.93
C0.99
D1.65
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.486 6497 -
Rfree-0 -
obs--100 %

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