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- EMDB-41040: Human HCN1 F186C S264C C309A bound to cAMP, reconstituted in LMNG... -

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Basic information

Entry
Database: EMDB / ID: EMD-41040
TitleHuman HCN1 F186C S264C C309A bound to cAMP, reconstituted in LMNG + SPL
Map data
Sample
  • Complex: Human HCN1 Channel
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
  • Ligand: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
KeywordsMembrane Protein / Ion Channel / TRANSPORT PROTEIN
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 / apical protein localization / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / regulation of membrane depolarization ...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 / apical protein localization / voltage-gated monoatomic cation channel activity / voltage-gated sodium channel activity / regulation of membrane depolarization / voltage-gated potassium channel activity / potassium channel activity / sodium ion transmembrane transport / neuronal action potential / presynaptic active zone membrane / cAMP binding / 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 / Cyclic nucleotide-binding domain superfamily ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsBurtscher V / Mount J / Cowgill J / Chang Y / Bickel K / Yuan P / Chanda B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS101723 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143440 United States
CitationJournal: To Be Published
Title: Structural Basis for Hyperpolarization-dependent Opening of the Human HCN1 Channel
Authors: Burtscher V / Mount J / Cowgill J / Chang Y / Bickel K / Yuan P / Chanda B
History
DepositionJun 12, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41040.png

Downloads & links

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Map

FileDownload / File: emd_41040.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.016 Å		1.09 Å/pix.
x 256 pix.
= 278.016 Å		1.09 Å/pix.
x 256 pix.
= 278.016 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.086 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.49021685 - 0.72741
Average (Standard dev.)0.0008381333 (±0.016256053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41040_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_41040_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_41040_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human HCN1 Channel

EntireName: Human HCN1 Channel
Components
  • Complex: Human HCN1 Channel
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
  • Ligand: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

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Supramolecule #1: Human HCN1 Channel

SupramoleculeName: Human HCN1 Channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homomeric Tetramer
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium/sodium hyperpolarization-activated cyclic nucleotide-ga...

MacromoleculeName: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.839758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGGGKPNSS SNSRDDGNSV FPAKASATGA GPAAAEKRLG TPPGGGGAGA KEHGNSVCFK VDGGGGGGGG GGGGEEPAGG FEDAEGPRR QYGFMQRQFT SMLQPGVNKF SLRMFGSQKA VEKEQERVKT AGFWIIHPYS DFRFYWDLIM LIMMVGNLVI I PVGITFFT ...String:
MEGGGKPNSS SNSRDDGNSV FPAKASATGA GPAAAEKRLG TPPGGGGAGA KEHGNSVCFK VDGGGGGGGG GGGGEEPAGG FEDAEGPRR QYGFMQRQFT SMLQPGVNKF SLRMFGSQKA VEKEQERVKT AGFWIIHPYS DFRFYWDLIM LIMMVGNLVI I PVGITFFT EQTTTPWIIF NVASDTVCLL DLIMNFRTGT VNEDSSEIIL DPKVIKMNYL KSWFVVDFIS SIPVDYIFLI VE KGMDSEV YKTARALRIV RFTKILCLLR LLRLSRLIRY IHQWEEIFHM TYDLASAVVR IFNLIGMMLL LAHWDGCLQF LVP LLQDFP PDCWVSLNEM VNDSWGKQYS YALFKAMSHM LCIGYGAQAP VSMSDLWITM LSMIVGATCY AMFVGHATAL IQSL DSSRR QYQEKYKQVE QYMSFHKLPA DMRQKIHDYY EHRYQGKIFD EENILNELND PLREEIVNFN CRKLVATMPL FANAD PNFV TAMLSKLRFE VFQPGDYIIR EGAVGKKMYF IQHGVAGVIT KSSKEMKLTD GSYFGEICLL TKGRRTASVR ADTYCR LYS LSVDNFNEVL EEYPMMRRAF ETVAIDRLDR IGKKNSILLQ KFQKDLNTGV FNNQENEILK QIVKHDREMV QAIAPIN YP QMTTLNSTSS TTTPTSRMRT QSPPVYTATS LSHSNLHSPS PSTQTPQPSA ILSPCSYTTA VCSPPVQSPL AARTFHYA S PTASQLSLMQ QQPQQQVQQS QPPQTQPQQP SPQPQTPGSS TPKNEVHKST QALHNTNLTR EVRPLSASQP SLPHEVSTL ISRPHPTVGE SLASIPQPVT AVPGTGLQAG GRSTVPQRVT LFRQMSSGAI PPNRGVPPAP PPPAAALPRE SSSVLNTDPD AEKPRFASN L

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

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Macromolecule #2: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

MacromoleculeName: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CMP
Molecular weightTheoretical: 329.206 Da
Chemical component information

ChemComp-CMP:
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic adenosine 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

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMKClPotassium Chloride
20.0 mMTrizma Base
0.01 mMCyclic adenosine monophosphate
0.2 mMHgClMercury Chloride
0.025 mMLauryl Maltose Neopentyl Glycol
7.5 uMSoy Polar Lipids
5.0 uMCholesterol Hemisuccinate
1.0 mMFluorinated Fos-Choline 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 53.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 167527
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8t4m

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 42000 / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 122422
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8t4m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8t4y:
Human HCN1 F186C S264C C309A bound to cAMP, reconstituted in LMNG + SPL

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