Ion channels 3D structures

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3D structures of ion channels

Updated on 06-October-2025 {{#tree:id=OrganizedByTopic|openlevels=0|

  • Calcium channel
    • 2d46 – hVDCC  4a – NMR – human
    • 6nq0, 6nq1, 6nq2 – hTpc2 – Cryo EM
    • 8if4 – hCav alpha-2+delta-1 – Cryo EM
    • 8if3 – hCav alpha-2+delta-1 + drug – Cryo EM
    • 2be6, 2f3y, 2f3z – hCav1.2  1C subunit+calmodulin
    • 3oxq - hCav2.1  1C subunit IQ domain+hCalmodulin
    • 2vay, 3oxq – hCav1.1  1S subunit IQ domain+hCalmodulin
    • 8eoi – hCav1.2 in EMC chaperone – Cryo EM
    • 8fd7 – hCav1.2 + drug – Cryo EM
    • 8eog – hCav1.2 + Leu – Cryo EM
    • 7uhg – hCav1.3 – Cryo EM
    • 7uhf, 8e59, 8e5a, 8e5b – hCav1.3 + drug – Cryo EM
    • 7vfs – hCav2.2 alpha-2+delta-1+beta1 – Cryo EM
    • 7vfu, 7vfv, 7vfw – hCav2.2 alpha-2+delta-1+beta1 + blocker – Cryo EM
    • 7miy – hCav2.2C – Cryo EM
    • 7mix – hCav2.2C + conotoxin – Cryo EM
    • 7xlq, 8epl, 8epm – hCav2.3 – Cryo EM
    • 6kzo – hCav3.1C – Cryo EM
    • 6kzp – hCav3.1C + antagonist – Cryo EM
    • 7wli – hCav3.3 – Cryo EM
    • 7wlj, 7wlk, 7wll – hCav3.3 + drug – Cryo EM
    • 6jp5, 6jp8, 7jpk, 7jpl, 7jpv, 7jpw, 7jpx – rCav1.1 – rabbit – Cryo EM
    • 6jpa, 6jpb – rCav1.1 + blocker – Cryo EM
    • 8e56, 8e57, 8e58 – rCav1.1 + drug – Cryo EM
    • 3bxx – rCav2.1  1A subunit+calmodulin
    • 3bxl - rCav2.3  1E subunit+calmodulin
    • 1t0h – rVDCC  2A subunit
    • 1t0j – rVDCC  2A+ 1C
    • 1vyt - rVDCC  3+ 1C
    • 1vyu – rVDCC  3
    • 1vyv - rVDCC  4
    • 6hw2 - rVDCC  4 + chromobox protein
    • 1t3l - rVDCC  2+ 1S
    • 1t3s - rVDCC  2
    • 3dve, 3dvj, 3dvk, 3dvm, 3g43 - rCav2.2  1B subunit+hCalmodulin
    • 4dex - rCav2.2  1B +  2 subunits
    • 4dey - rCav2.2  1C +  2 subunits
    • 6byo – rCav1.1  1S
    • 5gjw – rCav1.1  2/d 1 +  1S +  1 – Cryo EM
    • 3jbr, 5gjv – rCav1.1  2/d 1 +  1S +  1 + g 1 – Cryo EM
    • 5v2p, 5v2q - raCav1.2  1C +  2 - rat
    • 7qhh - raVDCC g 8 + glutamate receptor 1 – Cryo EM
    • 5kk2, 5vov, 5vou, 5vot - raVDCC g 2 + glutamate receptor 2 – Cryo EM
    • 6njl, 6njm, 6njn - raVDCC g 2 + glutamate receptor 1 + glutamate receptor 2 + a’/c’ auxiliary protein + antibody – Cryo EM
    • 6qkc, 6qkz, 7ocd - raVDCC g 8 + glutamate receptor 1 + glutamate receptor 2 – Cryo EM
    • 7oca, 7oce, 7ocf - raVDCC g 8 + glutamate receptor 1 + glutamate receptor 2 + CNIH-2 – Cryo EM
    • 8e0e – raCav L-type  2 + nanobody
    • 6c96, 6c9a – mTpc1 - mouse – Cryo EM
    • 4zw2 – mVDCC  1S peptide +  1
    • 7lep - mVDCC g 8 + glutamate receptor 2 + AMPAR subunits + CNIH-2 – Cryo EM
    • 8dam – mCav L-type  1 + nanobody
    • 5dqq, 5e1j, 5tua, 7fhk, 7fhl – AtTpc1 – Arabidopsis thaliana
    • 6cx0 – AtTpc1 (mutant)
    • 6e1m, 6e1n, 6e1p, 7fhn, 7fho, 7tbg, 7tdd, 7tde, 7tdf – AtTpc1 (mutant) – Cryo EM
    • 6e1k – AtTpc1 + antibody – Cryo EM
    • 6ijz, 6mgv, 6mgw – AtOsca1.2 – Cryo EM
    • 4mtf, 4mtg, 4mto – AbCaV + Ca – Arcobacter butzleri
  • Sodium channel; Domains – extracellular 30-157
    • 7dtd - hNaV 1.1 + hNav beta 4 – Cryo EM
    • 6agf - hNaV 1 + hNav 1.4 – Cryo EM
    • 2kav, 2kbi – hNaV 1.2 C-terminal EF-hand domain – NMR
    • 7w77, 7w7f – hNaV 1.3 beta1+beta2 + hNaV type 3 subunit alpha – Cryo EM
    • 5fdy, 5feb - hNaV 2 extracellular domain (mutant)
    • 6vrr - hNaV 2 (mutant)
    • 4l1d - hNaV 3 extracellular domain
    • 4mz2 - hNaV 4 extracellular domain
    • 4mz3, 6vsv - hNaV 4 extracellular domain (mutant)
    • 6bqn – hENaC alpha+beta+gamma subunits – Cryo EM
    • 7dtc – hNaV 1.5 (mutant) – Cryo EM
    • 7l83 – hNaV 1.5 1597-1633 - NMR
    • 8fhd – hNaV 1.6 – Cryo EM
    • 8gz1 – hNaV 1.6 beta1+beta2 + hNaV type 8 subunit alpha – Cryo EM
    • 7xvf – hNaV 1.7 (mutant) – Cryo EM
    • 7w9l, 7w9t – hNaV 1.7 (mutant) + beta-1 + beta-2 – Cryo EM
    • 7w9k – hNaV 1.7 beta-1 + beta-2 – Cryo EM
    • 7wfw – hNaV 1.8 – Cryo EM
    • 7tj8 – hNaV type 7 alpha – Cryo EM
    • 7tj9 – hNaV type 7 alpha + beta-3 – Cryo EM
    • 1byy – rNaCh IIA inactivation fragment
    • 5jr0 – rNaV 1.4
    • 7fbs – raNaV 1.5 (mutant) – Cryo EM
    • 6uz3 – raNaV 5 - Cryo EM
    • 1qg9 – raNaCh IIA second repeat – NMR
    • 5ayq, 5xaw, 5xax - mNaV 4 residues 30-160
    • 5xsy – eeNaV 1.4 + beta 1 – electric eel - Cryo EM
    • 5x0m – coNaCh - cockroach
    • 4bgn – NaCh – Caldalkalibacillus thermarum – Cryo EM
    • 4lto, 4ltp, 4ltq, 5hk7 – AeNaCh pore + cytoplasmic domains – Alkalilimnicola ehrlichii
    • 4ltr, 5hk6, 5hkd, 5kj8 – AeNaCh pore + cytoplasmic domains (mutant)
    • 5iwn, 7pgh – AeNaCh pore domain
    • 7x5v – NaV – Emiliania huxleyi - Cryo EM
  • Sodium channel complex
    • 6j8e - hNaV 2 + hNav 1.2 + Mu-conotoxin – Cryo EM
    • 6j8g, 6j8h, 6j8i, 6j8j - hNaV 2 + hNaV 1 + hNav 1.7 + toxin – Cryo EM
    • 6mba, 6mc9 – hNaV 1.4 C terminal + calmodulin
    • 6wth – hENaC alpha+beta+gamma subunits + antibody – Cryo EM
    • 6lqa – hNaV 1.5 + quinidine - Cryo EM
    • 4djc, 4ovn, 5dbr, 6mud – hNaV 1.5 C terminal + calmodulin
    • 4dck, 4jq0 – hNaV 1.5 C terminal + calmodulin + fibroblast growth factor
    • 4jpz – hNaV 1.2 C terminal + calmodulin + fibroblast growth factor 13
    • 8gz2 – hNaV 1.6 beta1+beta2 + hNaV type 8 subunit alpha + toxin – Cryo EM
    • 7w9m, 7w9p – hNaV 1.7 beta1+beta2 + hNaV type 9 subunit alpha + toxin – Cryo EM
    • 7xm9, 7xmf, 7xmg – hNaV 1.7 beta1+beta2 + hNaV type 9 subunit alpha + inhibitor – Cryo EM
    • 7we4, 7wel, 7wfr – hNaV 1.8 + inhibitor – Cryo EM
    • 6mue – raNaV 1.4 + calmodulin
    • 6uz0 – raNaV 5 + flecainide - Cryo EM
    • 7k18 – raNaV 5 + toxin - Cryo EM
    • 6a90, 6a91, 6a95 – coNaCh + toxin – Cryo EM
    • 7pg8, 7pgb – AeNaCh pore + antibody


  • Sodium channel, pre-activated. NavAb
  • Sodium channel, activated. NavMs

NH4+ channel

MscL and MscS

Chloride channel or H(+)/Cl(-) exchange transporter ClcA or human proton-activated chloride channel PAC or CLIC


Anion Channel (Outer mitochondrial membrane protein porin 1)

Ligand-gated ion channel

Cyclic Nucleotide-Gated channel

    • 7lg1 – hCNGA1 (mutant) – Cryo EM
    • 7lft – hCNGA1 + cGMP – Cryo EM
    • 7lfw, 7lfx, 7lfy – hCNGA1 (mutant) + cGMP – Cryo EM
    • 7rh9, 7rhl – hCNGA1 + CNGB1 – Cryo EM
    • 7rhg, 7rhh, 7rhi, 7rhj, 7rhk – hCNGA1 + CNGB1 + cGMP – Cryo EM
    • 8bx7 – bCNGA1 + CNGB1 + cGMP – Cryo EM
    • 7rhs – hCNGA3 + CNGB3 – Cryo EM
    • 3swf - bCNGC CLZ domain
    • 2zd9, 3beh – MlCNGC - Mesorhizobium loti
    • 4chv, 4chw – MlCNGC – Cryo EM
    • 2ptm – CNGC C-terminal – Strongylocentrotus purpuratus
    • 1vp6, 2kxl - MlCNGC ligand-binding domain
    • 1u12, 3clp, 3co2, 4muv - MlCNGC ligand-binding domain (mutant)
    • 2k0g, 3cl1 - MlCNGC ligand-binding domain + cyclic nucleotide
    • 5h3o – CeCNGC – Cryo EM
    • 6wej, 6wek, 6wel – CeCNGC + cGMP – Cryo EM
    • 6cju, 6vxz, 6vy0 – StCNGC + cAMP – Spitochaeta thermophila - Cryo EM
    • 6cjq – StCNGC - Cryo EM
    • 6cjt – StCNGC + cGMP - Cryo EM
  • Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel


    • 5u6o, 5u6p, 6uqf, 6uqg – hCNGC 1 – Cryo EM
    • 2mpf – hCNGC 2 ligand-binding domain - NMR
    • 3swy – hCNGC 3 CLZ domain
    • 6gyn – hCNGC 4 – Cryo EM
    • 6gyo – hCNGC 4 + cAMP – Cryo EM
    • 3otf – hCNGC 4 ligand-binding domain
    • 2mng – hCNGC 4 ligand-binding domain - NMR
    • 4hbn – hCNGC 4 ligand-binding domain (mutant)
    • 4kl1 – hCNGC 4 C terminal + nucleotide
    • 4nvp – hCNGC 4 ligand-binding domain + 7-CH-cAMP
    • 7nmn, 7np3 – rCNGC 4 – Cryo EM
    • 7np4 – rCNGC 4 + cAMP – Cryo EM
    • 3etq, 3ffq, 3u0z, 3u10, 3u11 – mCNGC C-terminal
    • 1q3e, 1q43, 1q5o – mCNGC 2 fragment + cyclic nucleotide
    • 2q0a – mCNGC C-terminal (mutant)
    • 3bpz – mCNGC ligand-binding domain (mutant)
    • 5khg, 5khh, 5khi, 5khj, 5khk – mCNGC 2 ligand-binding domain + nucleotide

Acid sensing ion channel

ATP-Gated P2X channel (AGC) or P2X purinoceptor

Proton channel or matrix protein 2

    • 2kj1, 2l0j - IVproton channel cytoplasmic domain – Influenza virus - NMR
    • 2kih, 2kwx – IVproton channel (mutant)
    • 3bkd, 3lbw, 4qk7, 4qkc, 4qkl, 4qkm, 5joo, 5ttc, 5um1 - IVproton channel transmembrane domain
    • 1mp6, 1nyj, 2kad, 6pvr, 6pvt - IVproton channel transmembrane domain – NMR
    • 4rwb, 4rwc, 5c02, 6mjh - IVproton channel transmembrane domain (mutant)
    • 2n70 - IVproton channel transmembrane domain (mutant) - NMR
    • 6bkk, 6bkl, 6bmz, 6boc, 6us8, 6us9 - IVproton channel transmembrane domain + drug
    • 2h95, 2kqt - IVproton channel transmembrane domain + drug - NMR
    • 2ly0 - IVproton channel transmembrane domain (mutant) + drug - NMR
    • 2rlf - IVproton channel + inhibitor – NMR
    • 3c9j, 6oug - IVproton channel transmembrane domain + inhibitor
    • 6nv1 - IVproton channel transmembrane domain (mutant) + inhibitor
    • 8bdz, 8ber - proton channel M2 – Hepatitis virus – Cryo EM

Voltage-gated hydrogen channel (VGHC)

    • 3a2a – hVGHC C-terminal – NMR
    • 5oqk – hVGHC residues 82-226 - NMR
    • 3wkv – mVGHC
    • 3vmx, 3vmy, 3vmz – mVGHC C-terminal
    • 3vn0, 3vyi – mVGHC C-terminal (mutant)
  • Synthetic ion channel
  • Transient receptor potential cation channel, vanilloid subfamily (TRPV)
  • TRPV1 or capsaicin receptor
  • TRPV2
  • TRPV3
  • TRPV4
    • 7aa5 – hTRPV4 + agonist – Cryo EM
    • 4dx1, 4dx2 – hTRPV4 ankyrin repeat domain 149-397
    • 6c8f, 6c8g, 6c8h – fTRPV4 (mutant) – frog
    • 6bbj – fTRPV4 – Cryo EM
    • 3jxi, 3jxj, 3w9g – cTRPV4 ankyrin repeat domain 133-382
    • 3w9f – cTRPV4 ankyrin repeat domain + inositol-3-phosphate
  • TRPV5
  • TRPV6
  • Transient receptor potential cation channel (TRPM)
  • TRPM2
  • TRPM3
  • Short transient receptor potential channel 5 (TRPC5)
  • TRPC5
  • Glycerol facilitator

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Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman, Jaime Prilusky

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