[English] 日本語
Yorodumi
- EMDB-35606: Cryo-EM structure of human HCN3 channel with cilobradine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35606
TitleCryo-EM structure of human HCN3 channel with cilobradine
Map data
Sample
  • Complex: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
  • Ligand: 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl]-7,8-dimethoxy-2,5-dihydro-1~{H}-3-benzazepin-4-one
Keywordshuman HCN3 channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


cone cell pedicle / HCN channels / HCN channel complex / regulation of membrane depolarization / cellular response to dopamine / voltage-gated sodium channel activity / voltage-gated potassium channel activity / cAMP binding / potassium ion transmembrane transport / sodium ion transmembrane transport ...cone cell pedicle / HCN channels / HCN channel complex / regulation of membrane depolarization / cellular response to dopamine / voltage-gated sodium channel activity / voltage-gated potassium channel activity / cAMP binding / potassium ion transmembrane transport / sodium ion transmembrane transport / regulation of membrane potential / axon / neuronal cell body / dendrite / plasma membrane
Similarity search - Function
Ion transport N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 N-terminal / Ion transport protein N-terminal / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsYu B / Lu QY / Li J / Zhang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human HCN3 channel with cilobradine
Authors: Yu B / Lu QY / Li J / Zhang J
History
DepositionMar 10, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35606.png

Downloads & links

-
Map

FileDownload / File: emd_35606.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 400 pix.
= 210.4 Å		0.53 Å/pix.
x 400 pix.
= 210.4 Å		0.53 Å/pix.
x 400 pix.
= 210.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.526 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.02984527 - 0.111165665
Average (Standard dev.)0.0049785757 (±0.008687585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 210.40001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35606_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : otassium/sodium hyperpolarization-activated cyclic nucleotide-gat...

EntireName: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
Components
  • Complex: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
    • Protein or peptide: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
  • Ligand: 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl]-7,8-dimethoxy-2,5-dihydro-1~{H}-3-benzazepin-4-one

-
Supramolecule #1: otassium/sodium hyperpolarization-activated cyclic nucleotide-gat...

SupramoleculeName: otassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.142922 KDa
Recombinant expressionOrganism: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
SequenceString: MEAEQRPAAG ASEGATPGLE AVPPVAPPPA TAASGPIPKS GPEPKRRHLG TLLQPTVNKF SLRVFGSHKA VEIEQERVKS AGAWIIHPY SDFRFYWDLI MLLLMVGNLI VLPVGITFFK EENSPPWIVF NVLSDTFFLL DLVLNFRTGI VVEEGAEILL A PRAIRTRY ...String:
MEAEQRPAAG ASEGATPGLE AVPPVAPPPA TAASGPIPKS GPEPKRRHLG TLLQPTVNKF SLRVFGSHKA VEIEQERVKS AGAWIIHPY SDFRFYWDLI MLLLMVGNLI VLPVGITFFK EENSPPWIVF NVLSDTFFLL DLVLNFRTGI VVEEGAEILL A PRAIRTRY LRTWFLVDLI SSIPVDYIFL VVELEPRLDA EVYKTARALR IVRFTKILSL LRLLRLSRLI RYIHQWEEIF HM TYDLASA VVRIFNLIGM MLLLCHWDGC LQFLVPMLQD FPPDCWVSIN HMVNHSWGRQ YSHALFKAMS HMLCIGYGQQ APV GMPDVW LTMLSMIVGA TCYAMFIGHA TALIQSLDSS RRQYQEKYKQ VEQYMSFHKL PADTRQRIHE YYEHRYQGKM FDEE SILGE LSEPLREEII NFTCRGLVAH MPLFAHADPS FVTAVLTKLR FEVFQPGDLV VREGSVGRKM YFIQHGLLSV LARGA RDTR LTDGSYFGEI CLLTRGRRTA SVRADTYCRL YSLSVDHFNA VLEEFPMMRR AFETVAMDRL LRIGKKNSIL QRKRSE PSP GSSGGIMEQH LVQHDRDMAR GVRGRAPSTG AQLSGKPVLW EPLVHAPLQA AAVTSNVAIA LTHQRGPLPL SPDSPAT LL ARSAWRSAGS PASPLVPVRA GPWASTSRLP APPARTLHAS LSRAGRSQVS LLGPPPGGGG RRLGPRGRPL SASQPSLP Q RATGDGSPGR KGSGSERLPP SGLLAKPPRT AQPPRPPVPE PATPRGLQLS ANM

UniProtKB: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3

-
Macromolecule #2: 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl...

MacromoleculeName: 3-[[(3~{S})-1-[2-(3,4-dimethoxyphenyl)ethyl]piperidin-3-yl]methyl]-7,8-dimethoxy-2,5-dihydro-1~{H}-3-benzazepin-4-one
type: ligand / ID: 2 / Number of copies: 4 / Formula: VXI
Molecular weightTheoretical: 482.612 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121387
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more