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- EMDB-25414: Structure of human Kv1.3 with Fab-ShK fusion -

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Basic information

Entry
Database: EMDB / ID: EMD-25414
TitleStructure of human Kv1.3 with Fab-ShK fusion
Map dataHuman Kv1.3 with Fab-ShK
Sample
  • Complex: Kv1.3 with Fab-ShK
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 3,Green fluorescent protein fusion
    • Protein or peptide: Fab-ShK fusion, heavy chain
    • Protein or peptide: Fab-ShK fusion, light chain
  • Ligand: POTASSIUM ION
Keywordsion channel / IMMUNE SYSTEM
Function / homology
Function and homology information


voltage-gated monoatomic ion channel activity / corpus callosum development / delayed rectifier potassium channel activity / Voltage gated Potassium channels / outward rectifier potassium channel activity / optic nerve development / action potential / calyx of Held / voltage-gated potassium channel activity / voltage-gated potassium channel complex ...voltage-gated monoatomic ion channel activity / corpus callosum development / delayed rectifier potassium channel activity / Voltage gated Potassium channels / outward rectifier potassium channel activity / optic nerve development / action potential / calyx of Held / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / bioluminescence / generation of precursor metabolites and energy / potassium ion transport / protein homooligomerization / presynaptic membrane / postsynaptic membrane / membrane raft / axon / glutamatergic synapse / perinuclear region of cytoplasm / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / Green fluorescent protein, GFP / SKP1/BTB/POZ domain superfamily ...Potassium channel, voltage dependent, Kv1.3 / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / Green fluorescent protein, GFP / SKP1/BTB/POZ domain superfamily / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily A member 3 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsMeyerson JR / Selvakumar P
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Commun / Year: 2022
Title: Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators.
Authors: Purushotham Selvakumar / Ana I Fernández-Mariño / Nandish Khanra / Changhao He / Alice J Paquette / Bing Wang / Ruiqi Huang / Vaughn V Smider / William J Rice / Kenton J Swartz / Joel R Meyerson /
Abstract: The Kv1.3 potassium channel is expressed abundantly on activated T cells and mediates the cellular immune response. This role has made the channel a target for therapeutic immunomodulation to block ...The Kv1.3 potassium channel is expressed abundantly on activated T cells and mediates the cellular immune response. This role has made the channel a target for therapeutic immunomodulation to block its activity and suppress T cell activation. Here, we report structures of human Kv1.3 alone, with a nanobody inhibitor, and with an antibody-toxin fusion blocker. Rather than block the channel directly, four copies of the nanobody bind the tetramer's voltage sensing domains and the pore domain to induce an inactive pore conformation. In contrast, the antibody-toxin fusion docks its toxin domain at the extracellular mouth of the channel to insert a critical lysine into the pore. The lysine stabilizes an active conformation of the pore yet blocks ion permeation. This study visualizes Kv1.3 pore dynamics, defines two distinct mechanisms to suppress Kv1.3 channel activity with exogenous inhibitors, and provides a framework to aid development of emerging T cell immunotherapies.
History
DepositionNov 11, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25414.png

Downloads & links

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Map

FileDownload / File: emd_25414.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Kv1.3 with Fab-ShK
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 374.88 Å		0.85 Å/pix.
x 440 pix.
= 374.88 Å		0.85 Å/pix.
x 440 pix.
= 374.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.227
Minimum - Maximum-1.582851 - 2.755387
Average (Standard dev.)0.001894652 (±0.03974029)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Kv1.3 with Fab-ShK

EntireName: Kv1.3 with Fab-ShK
Components
  • Complex: Kv1.3 with Fab-ShK
    • Protein or peptide: Potassium voltage-gated channel subfamily A member 3,Green fluorescent protein fusion
    • Protein or peptide: Fab-ShK fusion, heavy chain
    • Protein or peptide: Fab-ShK fusion, light chain
  • Ligand: POTASSIUM ION

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Supramolecule #1: Kv1.3 with Fab-ShK

SupramoleculeName: Kv1.3 with Fab-ShK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium voltage-gated channel subfamily A member 3,Green fluore...

MacromoleculeName: Potassium voltage-gated channel subfamily A member 3,Green fluorescent protein fusion
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 95.0185 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDERLSLLRS PPPPSARHRA HPPQRPASSG GAHTLVNHGY AEPAAGRELP PDMTVVPGDH LLEPEVADGG GAPPQGGCGG GGCDRYEPL PPSLPAAGEQ DCCGERVVIN ISGLRFETQL KTLCQFPETL LGDPKRRMRY FDPLRNEYFF DRNRPSFDAI L YYYQSGGR ...String:
MDERLSLLRS PPPPSARHRA HPPQRPASSG GAHTLVNHGY AEPAAGRELP PDMTVVPGDH LLEPEVADGG GAPPQGGCGG GGCDRYEPL PPSLPAAGEQ DCCGERVVIN ISGLRFETQL KTLCQFPETL LGDPKRRMRY FDPLRNEYFF DRNRPSFDAI L YYYQSGGR IRRPVNVPID IFSEEIRFYQ LGEEAMEKFR EDEGFLREEE RPLPRRDFQR QVWLLFEYPE SSGPARGIAI VS VLVILIS IVIFCLETLP EFRDEKDYPA STSQDSFEAA GNSTSGSRAG ASSFSDPFFV VETLCIIWFS FELLVRFFAC PSK ATFSRN IMNLIDIVAI IPYFITLGTE LAERQGNGQQ AMSLAILRVI RLVRVFRIFK LSRHSKGLQI LGQTLKASMR ELGL LIFFL FIGVILFSSA VYFAEADDPT SGFSSIPDAF WWAVVTMTTV GYGDMHPVTI GGKIVGSLCA IAGVLTIALP VPVIV SNFN YFYHRETEGE EQSQYMHVGS CQHLSSSAEE LRKARSNSTL SKSEYMVIEE GGMNHSAFPQ TPFKTGNSTA TCTTNN NPN SCVNIKKIFT DVSLEVLFQG PAAAMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK LICTTGK LP VPWPTLVTTL GYGLQCFARY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDTLVNRIE LKGIDFKE D GNILGHKLEY NYNSHNVYIT ADKQKNGIKA NFKIRHNIED GGVQLADHYQ QNTPIGDGPV LLPDNHYLSY QSKLSKDPN EKRDHMVLLE FVTAAGITLG MDELYKSAWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Potassium voltage-gated channel subfamily A member 3, Green fluorescent protein

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Macromolecule #2: Fab-ShK fusion, heavy chain

MacromoleculeName: Fab-ShK fusion, heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 29.417229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLREWGAG LLKPSETLSL TCAVYGGSFS DKYWSWIRQP PGKGLEWIGS INHSGSTNYN PSLKSRVTIS VDTSKNQFSL KLSSVTAAD TAVYYCTSVH QETKKYQSRS CIDTIPKSRC TAFQCKHSMK YRLSFCRKTC GTCSYTYNYE WHVDVWGQGL L VTVSSAST ...String:
QVQLREWGAG LLKPSETLSL TCAVYGGSFS DKYWSWIRQP PGKGLEWIGS INHSGSTNYN PSLKSRVTIS VDTSKNQFSL KLSSVTAAD TAVYYCTSVH QETKKYQSRS CIDTIPKSRC TAFQCKHSMK YRLSFCRKTC GTCSYTYNYE WHVDVWGQGL L VTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SS LGTQTYI CNVNHKPSNT KVDKKVEPKS CDK

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Macromolecule #3: Fab-ShK fusion, light chain

MacromoleculeName: Fab-ShK fusion, light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 22.524752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAVLNQPSSV SGSLGQKVTI SCSGSSSNIG NNYVSWYQQL PGTAPKLLIY GDTKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYC ASAEDSSSNA VFGSGTTLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QAVLNQPSSV SGSLGQKVTI SCSGSSSNIG NNYVSWYQQL PGTAPKLLIY GDTKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYC ASAEDSSSNA VFGSGTTLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 3 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90267
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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