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- EMDB-35614: Herg1a-herg1b closed state 1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35614
TitleHerg1a-herg1b closed state 1
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


membrane repolarization during action potential / inward rectifier potassium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / monoatomic ion channel complex / regulation of heart rate by cardiac conduction
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
Potassium voltage-gated channel subfamily H member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Herg1a-herg1b closed state 1
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_35614.png

Downloads & links

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Map

FileDownload / File: emd_35614.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.29146668 - 0.49373448
Average (Standard dev.)0.00008101844 (±0.01071456)
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_35614_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_35614_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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: Potassium voltage-gated channel subfamily H member 2

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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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