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- EMDB-35607: Herg1a-herg1b open state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35607
TitleHerg1a-herg1b open state
Map data
Sample
  • Complex: Herg1a-herg1b channel
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 2
Keywordschannelrhodopsin / MEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization ...inward rectifier potassium channel complex / negative regulation of potassium ion export across plasma membrane / regulation of heart rate by hormone / Phase 3 - rapid repolarisation / membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / membrane repolarization / positive regulation of potassium ion transmembrane transport / delayed rectifier potassium channel activity / Voltage gated Potassium channels / inward rectifier potassium channel activity / potassium ion homeostasis / ventricular cardiac muscle cell action potential / membrane depolarization during action potential / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of potassium ion transmembrane transport / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / voltage-gated potassium channel complex / cardiac muscle contraction / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / cellular response to xenobiotic stimulus / scaffold protein binding / transcription cis-regulatory region binding / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ERG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Potassium channel, voltage-dependent, ERG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated inwardly rectifying potassium channel KCNH2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Herg1a-herg1b open state
Authors: Zhang MF
History
DepositionMar 10, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35607.png

Downloads & links

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Map

FileDownload / File: emd_35607.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.)
0.85 Å/pix.
x 400 pix.
= 339.6 Å		0.85 Å/pix.
x 400 pix.
= 339.6 Å		0.85 Å/pix.
x 400 pix.
= 339.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.5618765 - 0.94261813
Average (Standard dev.)0.000012671263 (±0.014361326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 339.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35607_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35607_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Herg1a-herg1b channel

EntireName: Herg1a-herg1b channel
Components
  • Complex: Herg1a-herg1b channel
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 2

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Supramolecule #1: Herg1a-herg1b channel

SupramoleculeName: Herg1a-herg1b channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium voltage-gated channel subfamily H member 2

MacromoleculeName: Potassium voltage-gated channel subfamily H member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 126.802727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPVRRGHVAP QNTFLDTIIR KFEGQSRKFI IANARVENCA VIYCNDGFCE LCGYSRAEVM QRPCTCDFLH GPRTQRRAAA QIAQALLGA EERKVEIAFY RKDGSCFLCL VDVVPVKNED GAVIMFILNF EVVMEKDMVG SPAHDTNHRG PPTSWLAPGR A KTFRLKLP ...String:
MPVRRGHVAP QNTFLDTIIR KFEGQSRKFI IANARVENCA VIYCNDGFCE LCGYSRAEVM QRPCTCDFLH GPRTQRRAAA QIAQALLGA EERKVEIAFY RKDGSCFLCL VDVVPVKNED GAVIMFILNF EVVMEKDMVG SPAHDTNHRG PPTSWLAPGR A KTFRLKLP ALLALTARES SVRSGGAGGA GAPGAVVVDV DLTPAAPSSE SLALDEVTAM DNHVAGLGPA EERRALVGPG SP PRSAPGQ LPSPRAHSLN PDASGSSCSL ARTRSRESCA SVRRASSADD IEAMRAGVLP PPPRHASTGA MHPLRSGLLN STS DSDLVR YRTISKIPQI TLNFVDLKGD PFLASPTSDR EIIAPKIKER THNVTEKVTQ VLSLGADVLP EYKLQAPRIH RWTI LHYSP FKAVWDWLIL LLVIYTAVFT PYSAAFLLKE TEEGPPATEC GYACQPLAVV DLIVDIMFIV DILINFRTTY VNANE EVVS HPGRIAVHYF KGWFLIDMVA AIPFDLLIFG SGSEELIGLL KTARLLRLVR VARKLDRYSE YGAAVLFLLM CTFALI AHW LACIWYAIGN MEQPHMDSRI GWLHNLGDQI GKPYNSSGLG GPSIKDKYVT ALYFTFSSLT SVGFGNVSPN TNSEKIF SI CVMLIGSLMY ASIFGNVSAI IQRLYSGTAR YHTQMLRVRE FIRFHQIPNP LRQRLEEYFQ HAWSYTNGID MNAVLKGF P ECLQADICLH LNRSLLQHCK PFRGATKGCL RALAMKFKTT HAPPGDTLVH AGDLLTALYF ISRGSIEILR GDVVVAILG KNDIFGEPLN LYARPGKSNG DVRALTYCDL HKIHRDDLLE VLDMYPEFSD HFWSSLEITF NLRDTNMIPG SPGSTELEGG FSRQRKRKL SFRRRTDKDT EQPGEVSALG PGRAGAGPSS RGRPGGPWGE SPSSGPSSPE SSEDEGPGRS SSPLRLVPFS S PRPPGEPP GGEPLMEDCE KSSDTCNPLS GAFSGVSNIF SFWGDSRGRQ YQELPRCPAP TPSLLNIPLS SPGRRPRGDV ES RLDALQR QLNRLETRLS ADMATVLQLL QRQMTLVPPA YSAVTTPGPG PTSTSPLLPV SPLPTLTLDS LSQVSQFMAC EEL PPGAPE LPQEGPTRRL SLPGQLGALT SQPLHRHGSD PGS

UniProtKB: Voltage-gated inwardly rectifying potassium channel KCNH2

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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