9ITI: Sodium channel protein type 9 subunit alpha

Nav1.7 with mutations that eliminate beta1 binding. Determined by electron microscopy at 2.92 Å resolution. Released 20 Aug 2025.

Method
Electron microscopy
Resolution
2.92 Å
Organism
Homo sapiens
Chains
1
Atoms
11,086
Mol. weight
245.99 kDa
Ligands
Y01, PCW, 1PW, LPE
Released
20 Aug 2025

Explore 9ITI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ITI contains 73 α-helices and 18 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 73 helices, 18 β-strands

ElementResiduesLengthSheet
β-strand1411
α-helix17-3317
α-helix48-503
β-strand5812
α-helix59-602
α-helix61-633
α-helix65-673
α-helix68-703
β-strand7511
β-strand88-9141
β-strand9612
β-strand97-10041
α-helix1041
β-strand10513
β-strand10913
α-helix114-12310
α-helix126-14318
α-helix152-17423
α-helix183-1853
α-helix187-20418
α-helix210-2156
α-helix216-2238
α-helix224-2274
α-helix231-24313
α-helix246-26722
α-helix270-2723
β-strand273-27754
α-helix287-2904
α-helix297-3026
β-strand30314
β-strand328-33254
α-helix338-3403
α-helix347-35812
α-helix363-37412
α-helix376-3783
α-helix379-3857
α-helix386-3927
α-helix393-42432
α-helix729-74012
α-helix743-76119
α-helix770-79728
α-helix800-8034
α-helix807-82418
α-helix834-84613
α-helix850-86314
α-helix867-89428
α-helix896-8983
α-helix913-92513
α-helix929-93911
α-helix941-97333
α-helix987-101327
α-helix1176-119015
α-helix1192-120817
α-helix1209-12113
α-helix1220-124829
α-helix1250-12545
α-helix1257-127822
α-helix1284-12918
α-helix1292-130211
α-helix1305-131612
α-helix1318-134326
β-strand1349-135245
β-strand1357-135825
α-helix1359-13602
β-strand136616
α-helix1367-137610
β-strand1380-138345
α-helix1392-140312
α-helix1408-14169
β-strand142316
α-helix1431-14333
α-helix1434-14407
α-helix1441-14477
α-helix1448-146619
α-helix1476-148914
α-helix1491-150010
α-helix1503-151210
α-helix1515-153319
α-helix1541-156929
α-helix1572-15743
α-helix1577-159923
α-helix1606-16127
α-helix1613-16164
α-helix1617-16204
α-helix1621-16255
α-helix1628-166639
α-helix1684-169512
α-helix1700-17078
β-strand172017
β-strand172617
α-helix1732-176433

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 9 subunit alphaAprotein2030Homo sapiensQ15858 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9ITI_1 Sodium channel protein type 9 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTK
QSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLED
LDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTIL
TNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIV
FAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLS
VFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFLYLEGSKDALLCGF
STDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWERLYQQTLRAAGKT
YMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEA
EAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDA
EKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIRGSLFSARRSSRTSLFSF
KGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSSNISQASRSPPMLPVNGK
MHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSE
DMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCI
YFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIA
MDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIK
IIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSF
LIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLT
AIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENY
ISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESD
LENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEPEACFTD
GCVWRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIE
RKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANT
LGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSI
MGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYL
SLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSFFTLNLFIGVII
DNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAF
DISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVG
WNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFAL
MMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKWEDGINDMFNFETFGNSMICLFQITTS
AGWDGLLAPILNSKPPDCDPTLPNSNGSRGDCGNPSVGIFYFVSYIIISFLVVVNMYIAV
ILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAKP
NKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSYE
PITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKDMAFDNVN
ENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKK

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O44
PCW1,2-dioleoyl-sn-glycero-3-phosphocholineC44 H85 N O8 P5
1PW(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphateC20 H40 N O6 P1
LPE1-O-octadecyl-sn-glycero-3-phosphocholineC26 H57 N O6 P10
P5SO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serineC42 H82 N O10 P2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O62
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51

Water and common crystallization additives (NA) are not listed.

Primary citation

Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na v channels. Wu, T., Yang, X., Jin, X. et al. Proc Natl Acad Sci U S A (2025) 122:e2510355122-e2510355122. DOI 10.1073/pnas.2510355122 · PubMed

Other PDB entries of the same protein (UniProt Q15858 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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