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- EMDB-33860: Human KCNH5 pore dilation but the non-conducting state -

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Basic information

Entry
Database: EMDB / ID: EMD-33860
TitleHuman KCNH5 pore dilation but the non-conducting state
Map data
Sample
  • Complex: human KCNH5 pore dilation but the non-conducting state
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 5
  • Ligand: POTASSIUM ION
KeywordsPotassium Channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


delayed rectifier potassium channel activity / Voltage gated Potassium channels / voltage-gated potassium channel activity / regulation of G2/M transition of mitotic cell cycle / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / transmembrane transporter binding / calmodulin binding ...delayed rectifier potassium channel activity / Voltage gated Potassium channels / voltage-gated potassium channel activity / regulation of G2/M transition of mitotic cell cycle / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / transmembrane transporter binding / calmodulin binding / protein-containing complex binding / cell surface / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG / : / 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, EAG / : / 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 domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated delayed rectifier potassium channel KCNH5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang MF
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504100 China
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism underlying delayed rectifying in human voltage-mediated activation Eag2 channel.
Authors: Mingfeng Zhang / Yuanyue Shan / Duanqing Pei /
Abstract: The transmembrane voltage gradient is a general physico-chemical cue that regulates diverse biological function through voltage-gated ion channels. How voltage sensing mediates ion flows remains ...The transmembrane voltage gradient is a general physico-chemical cue that regulates diverse biological function through voltage-gated ion channels. How voltage sensing mediates ion flows remains unknown at the molecular level. Here, we report six conformations of the human Eag2 (hEag2) ranging from closed, pre-open, open, and pore dilation but non-conducting states captured by cryo-electron microscopy (cryo-EM). These multiple states illuminate dynamics of the selectivity filter and ion permeation pathway with delayed rectifier properties and Cole-Moore effect at the atomic level. Mechanistically, a short S4-S5 linker is coupled with the constrict sites to mediate voltage transducing in a non-domain-swapped configuration, resulting transitions for constrict sites of F464 and Q472 from gating to open state stabilizing for voltage energy transduction. Meanwhile, an additional potassium ion occupied at positions S6 confers the delayed rectifier property and Cole-Moore effects. These results provide insight into voltage transducing and potassium current across membrane, and shed light on the long-sought Cole-Moore effects.
History
DepositionJul 16, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33860.png

Downloads & links

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Map

FileDownload / File: emd_33860.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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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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-0.9192024 - 1.4536597
Average (Standard dev.)0.000921656 (±0.02900487)
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: #2

Fileemd_33860_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33860_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : human KCNH5 pore dilation but the non-conducting state

EntireName: human KCNH5 pore dilation but the non-conducting state
Components
  • Complex: human KCNH5 pore dilation but the non-conducting state
    • Protein or peptide: Potassium voltage-gated channel subfamily H member 5
  • Ligand: POTASSIUM ION

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Supramolecule #1: human KCNH5 pore dilation but the non-conducting state

SupramoleculeName: human KCNH5 pore dilation but the non-conducting state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Potassium voltage-gated channel subfamily H member 5

MacromoleculeName: Potassium voltage-gated channel subfamily H member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 112.011516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPGGKRGLVA PQNTFLENIV RRSSESSFLL GNAQIVDWPV VYSNDGFCKL SGYHRADVMQ KSSTCSFMYG ELTDKKTIEK VRQTFDNYE SNCFEVLLYK KNRTPVWFYM QIAPIRNEHE KVVLFLCTFK DITLFKQPIE DDSTKGWTKF ARLTRALTNS R SVLQQLTP ...String:
MPGGKRGLVA PQNTFLENIV RRSSESSFLL GNAQIVDWPV VYSNDGFCKL SGYHRADVMQ KSSTCSFMYG ELTDKKTIEK VRQTFDNYE SNCFEVLLYK KNRTPVWFYM QIAPIRNEHE KVVLFLCTFK DITLFKQPIE DDSTKGWTKF ARLTRALTNS R SVLQQLTP MNKTEVVHKH SRLAEVLQLG SDILPQYKQE APKTPPHIIL HYCAFKTTWD WVILILTFYT AIMVPYNVSF KT KQNNIAW LVLDSVVDVI FLVDIVLNFH TTFVGPGGEV ISDPKLIRMN YLKTWFVIDL LSCLPYDIIN AFENVDEGIS SLF SSLKVV RLLRLGRVAR KLDHYLEYGA AVLVLLVCVF GLVAHWLACI WYSIGDYEVI DEVTNTIQID SWLYQLALSI GTPY RYNTS AGIWEGGPSK DSLYVSSLYF TMTSLTTIGF GNIAPTTDVE KMFSVAMMMV GSLLYATIFG NVTTIFQQMY ANTNR YHEM LNNVRDFLKL YQVPKGLSER VMDYIVSTWS MSKGIDTEKV LSICPKDMRA DICVHLNRKV FNEHPAFRLA SDGCLR ALA VEFQTIHCAP GDLIYHAGES VDALCFVVSG SLEVIQDDEV VAILGKGDVF GDIFWKETTL AHACANVRAL TYCDLHI IK REALLKVLDF YTAFANSFSR NLTLTCNLRK RIIFRKISDV KKEEEERLRQ KNEVTLSIPV DHPVRKLFQK FKQQKELR N QGSTQGDPER NQLQVESRSL QNGASITGTS VVTVSQITPI QTSLAYVKTS ESLKQNNRDA MELKPNGGAD QKCLKVNSP IRMKNGNGKG WLRLKNNMGA HEEKKEDWNN VTKAESMGLL SEDPKSSDSE NSVTKNPLRK TDSCDSGITK SDLRLDKAGE ARSPLEHSP IQADAKHPFY PIPEQALQTT LQEVKHELKE DIQLLSCRMT ALEKQVAEIL KILSEKSVPQ ASSPKSQMPL Q VPPQIPCQ DIFSVSRPES PESDKDEIHF

UniProtKB: Voltage-gated delayed rectifier potassium channel KCNH5

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
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 opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44152
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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