9OT6: PI4KA complex

Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN). Determined by electron microscopy at 3.54 Å resolution. Released 3 Dec 2025.

Method
Electron microscopy
Resolution
3.54 Å
Organisms
Homo sapiens, Lama glama
Chains
8
Atoms
42,678
Mol. weight
768.41 kDa
Released
3 Dec 2025

Explore 9OT6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OT6 contains 288 α-helices and 60 β-strands across 8 chains. 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.

Chains A and B: 101 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix31-4313
α-helix48-492
α-helix50-5910
β-strand6411
β-strand6711
β-strand68-7032
α-helix72-8716
α-helix93-10513
α-helix107-1093
β-strand110-11232
α-helix128-14518
α-helix147-1493
α-helix150-16819
α-helix177-1782
α-helix179-1835
α-helix184-1929
α-helix204-2085
α-helix297-3004
α-helix326-33914
α-helix342-35817
α-helix370-38415
α-helix393-41119
α-helix434-44512
α-helix452-46615
α-helix479-49517
α-helix500-51213
α-helix516-5227
α-helix564-58320
α-helix587-60014
α-helix612-62615
α-helix634-64310
α-helix651-6533
α-helix654-66411
α-helix669-68517
α-helix705-71713
α-helix723-74018
α-helix767-7693
α-helix771-7788
α-helix782-7843
α-helix789-80517
α-helix817-82913
α-helix830-8323
α-helix841-8444
α-helix858-87215
α-helix876-8838
α-helix887-90620
α-helix913-9164
α-helix917-9204
α-helix923-9275
α-helix934-95118
α-helix958-97316
α-helix974-9763
α-helix981-99616
α-helix998-10003
α-helix1006-102015
β-strand1032-103323
β-strand1040-104123
α-helix1047-107125
α-helix1073-108311
α-helix1087-10926
α-helix1098-11069
β-strand111314
β-strand113414
α-helix1137-115620
α-helix1170-118314
α-helix1186-120116
α-helix1208-12158
α-helix1218-12203
α-helix1225-124016
α-helix1245-126218
α-helix1276-12783
α-helix1295-130814
α-helix1316-132510
α-helix1343-13453
α-helix1347-136115
α-helix1370-138314
α-helix1384-13863
α-helix1401-141515
α-helix1478-150730
α-helix1519-153214
α-helix1541-155010
α-helix1552-15576
α-helix1558-15603
α-helix1567-157812
α-helix1580-15823
α-helix1586-15894
α-helix1590-15923
α-helix1613-16142
α-helix1617-16215
α-helix1622-16243
α-helix1632-164211
α-helix1647-16526
α-helix1654-16596
α-helix1668-167912
α-helix1682-169413
β-strand169615
β-strand170415
α-helix1709-171911
α-helix1726-174823
α-helix1755-176713
β-strand1782-178766
β-strand1803-181196
α-helix1815-18206
β-strand1842-1851106
α-helix1857-187519
β-strand1886-189056
β-strand1893-189756
β-strand190417
α-helix1905-19128
α-helix1916-19249
α-helix1930-195324
β-strand1964-196527
β-strand1971-197227
α-helix1998-20036
α-helix2011-202717
α-helix2031-20399
α-helix2042-20443
α-helix2053-20597
α-helix2067-208014
Chains C and H: 0 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand6-9415
β-strand22-26515
β-strand35-41716
β-strand48-53616
β-strand59-61316
β-strand70-74515
β-strand79-83515
β-strand93-101916
β-strand110-114516
β-strand118-120316
Chains D and F: 31 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix135-15319
α-helix168-19528
α-helix218-23215
α-helix235-24612
α-helix249-2502
α-helix252-2543
α-helix255-26814
α-helix324-34017
α-helix353-37422
α-helix380-38910
α-helix397-41014
α-helix414-42613
α-helix432-44211
α-helix449-46012
α-helix467-48519
α-helix491-51020
α-helix515-52713
α-helix531-54414
α-helix549-56113
α-helix565-57814
α-helix584-59613
α-helix599-61618
α-helix690-70718
α-helix712-72211
α-helix730-74314
α-helix748-75912
α-helix765-77713
α-helix782-79312
α-helix798-80912
α-helix814-82815
α-helix836-8383
Chains E and G: 12 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix8-169
α-helix37-459
α-helix53-6210
α-helix69-768
α-helix79-9012
α-helix101-11313
β-strand123-125317
β-strand160-163417
α-helix177-18812
α-helix197-21014
α-helix216-2205
α-helix234-24714
α-helix254-27017
α-helix273-28311

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Phosphatidylinositol 4-kinase alphaA, Bprotein2104Homo sapiensP42356 (AlphaFold model)
EFR3 interfering Nanobody (F3IN)C, Hprotein165Lama glama
Tetratricopeptide repeat protein 7BD, Fprotein843Homo sapiensQ86TV6 (AlphaFold model)
HyccinE, Gprotein308Homo sapiensQ9BYI3 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9OT6_1 Phosphatidylinositol 4-kinase alpha (chains A, B)
GSMAAAPARGGGGGGGGGGGCSGSGSSASRGFYFNTVLSLARSLAVQRPASLEKVQKLLC
MCPVDFHGIFQLDERRRDAVIALGIFLIESDLQHKDCVVPYLLRLLKGLPKVYWVEESTA
RKGRGALPVAESFSFCLVTLLSDVAYRDPSLRDEILEVLLQVLHVLLGMCQALEIQDKEY
LCKYAIPCLIGISRAFGRYSNMEESLLSKLFPKIPPHSLRVLEELEGVRRRSFNDFRSIL
PSNLLTVCQEGTLKRKTSSVSSISQVSPERGMPPPSSPGGSAFHYFEASCLPDGTALEPE
YYFSTISSSFSVSPLFNGVTYKEFNIPLEMLRELLNLVKKIVEEAVLKSLDAIVASVMEA
NPSADLYYTSFSDPLYLTMFKMLRDTLYYMKDLPTSFVKEIHDFVLEQFNTSQGELQKIL
HDADRIHNELSPLKLRCQANAACVDLMVWAVKDEQGAENLCIKLSEKLQSKTSSKVIIAH
LPLLICCLQGLGRLCERFPVVVHSVTPSLRDFLVIPSPVLVKLYKYHSQYHTVAGNDIKI
SVTNEHSESTLNVMSGKKSQPSMYEQLRDIAIDNICRCLKAGLTVDPVIVEAFLASLSNR
LYISQESDKDAHLIPDHTIRALGHIAVALRDTPKVMEPILQILQQKFCQPPSPLDVLIID
QLGCLVITGNQYIYQEVWNLFQQISVKASSVVYSATKDYKDHGYRHCSLAVINALANIAA
NIQDEHLVDELLMNLLELFVQLGLEGKRASERASEKGPALKASSSAGNLGVLIPVIAVLT
RRLPPIKEAKPRLQKLFRDFWLYSVLMGFAVEGSGLWPEEWYEGVCEIATKSPLLTFPSK
EPLRSVLQYNSAMKNDTVTPAELSELRSTIINLLDPPPEVSALINKLDFAMSTYLLSVYR
LEYMRVLRSTDPDRFQVMFCYFEDKAIQKDKSGMMQCVIAVADKVFDAFLNMMADKAKTK
ENEEELERHAQFLLVNFNHIHKRIRRVADKYLSGLVDKFPHLLWSGTVLKTMLDILQTLS
LSLSADIHKDQPYYDIPDAPYRITVPDTYEARESIVKDFAARCGMILQEAMKWAPTVTKS
HLQEYLNKHQNWVSGLSQHTGLAMATESILHFAGYNKQNTTLGATQLSERPACVKKDYSN
FMASLNLRNRYAGEVYGMIRFSGTTGQMSDLNKMMVQDLHSALDRSHPQHYTQAMFKLTA
MLISSKDCDPQLLHHLCWGPLRMFNEHGMETALACWEWLLAGKDGVEVPFMREMAGAWHM
TVEQKFGLFSAEIKEADPLAASEASQPKPCPPEVTPHYIWIDFLVQRFEIAKYCSSDQVE
IFSSLLQRSMSLNIGGAKGSMNRHVAAIGPRFKLLTLGLSLLHADVVPNATIRNVLREKI
YSTAFDYFSCPPKFPTQGEKRLREDISIMIKFWTAMFSDKKYLTASQLVPPDNQDTRSNL
DITVGSRQQATQGWINTYPLSSGMSTISKKSGMSKKTNRGSQLHKYYMKRRTLLLSLLAT
EIERLITWYNPLSAPELELDQAGENSVANWRSKYISLSEKQWKDNVNLAWSISPYLAVQL
PARFKNTEAIGNEVTRLVRLDPGAVSDVPEAIKFLVTWHTIDADAPELSHVLCWAPTDPP
TGLSYFSSMYPPHPLTAQYGVKVLRSFPPDAILFYIPQIVQALRYDKMGYVREYILWAAS
KSQLLAHQFIWNMKTNIYLDEEGHQKDPDIGDLLDQLVEEITGSLSGPAKDFYQREFDFF
NKITNVSAIIKPYPKGDERKKACLSALSEVKVQPGCYLPSNPEAIVLDIDYKSGTPMQSA
AKAPYLAKFKVKRCGVSELEKEGLRCRSDSEDECSTQEADGQKISWQAAIFKVGDDCRQD
MLALQIIDLFKNIFQLVGLDLFVFPYRVVATAPGCGVIECIPDCTSRDQLGRQTDFGMYD
YFTRQYGDESTLAFQQARYNFIRSMAAYSLLLFLLQIKDRHNGNIMLDKKGHIIHIDFGF
MFESSPGGNLGWEPDIKLTDEMVMIMGGKMEATPFKWFMEMCVRGYLAVRPYMDAVVSLV
TLMLDTGLPCFRGQTIKLLKHRFSPNMTEREAANFIMKVIQSCFLSNRSRTYDMIQYYQN
DIPY
Sequence of entity 2 (C, H), FASTA
>9OT6_2 EFR3 interfering Nanobody (F3IN) (chains C, H)
MKYLLPTAAAGLLLLAAQPAMAMAQVQLQESGGGLVQAGGSLRLSCAASGTISASDYMGW
YRQAPGKERELVASIDGGGITNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCA
VDWILARYNFVIHYYWGQGTQVTVSSGSYPYDVPDYALEHHHHHH
Sequence of entity 3 (D, F), FASTA
>9OT6_3 Tetratricopeptide repeat protein 7B (chains D, F)
MATKKAGSRLETEIERCRSECQWERIPELVKQLSAKLIANDDMAELLLGESKLEQYLKEH
PLRQGASPRGPKPQLTEVRKHLTAALDRGNLKSEFLQESNLIMAKLNYVEGDYKEALNIY
ARVGLDDLPLTAVPPYRLRVIAEAYATKGLCLEKLPISSSTSNLHVDREQDVITCYEKAG
DIALLYLQEIERVILSNIQNRSPKPGPAPHDQELGFFLETGLQRAHVLYFKNGNLTRGVG
RFRELLRAVETRTTQNLRMTIARQLAEILLRGMCEQSYWNPLEDPPCQSPLDDPLRKGAN
TKTYTLTRRARVYSGENIFCPQENTEEALLLLLISESMANRDAVLSRIPEHKSDRLISLQ
SASVVYDLLTIALGRRGQYEMLSECLERAMKFAFEEFHLWYQFALSLMAAGKSARAVKVL
KECIRLKPDDATIPLLAAKLCMGSLHWLEEAEKFAKTVVDVGEKTSEFKAKGYLALGLTY
SLQATDASLRGMQEVLQRKALLAFQRAHSLSPTDHQAAFYLALQLAISRQIPEALGYVRQ
ALQLQGDDANSLHLLALLLSAQKHYHDALNIIDMALSEYPENFILLFSKVKLQSLCRGPD
EALLTCKHMLQIWKSCYNLTNPSDSGRGSSLLDRTIADRRQLNTITLPDFSDPETGSVHA
TSVAASRVEQALSEVASSLQSSAPKQGPLHPWMTLAQIWLHAAEVYIGIGKPAEATACTQ
EAANLFPMSHNVLYMRGQIAELRGSMDEARRWYEEALAISPTHVKSMQRLALILHQLGRY
SLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEASSPAVPFTIIP
RVL
Sequence of entity 4 (E, G), FASTA
>9OT6_4 Hyccin (chains E, G)
MFTSEKGVVEEWLSEFKTLPETSLPNYATNLKDKSSLVSSLYKVIQEPQSELLEPVCHQL
FEFYRSGEEQLLQFTLQFLPELIWCYLAVSASRNVHSSGCIEALLLGVYNLEIVDKQGHT
KVLSFTIPSLSKPSVYHEPSSIGSMALTESALSQHGLSKVVYSGPHPQREMLTAQNRFEV
LTFLLLCYNAALTYMPSVSLQSLCQICSRICVCGYPRQHVRKYKGISSRIPVSSGFMVQM
LTGIYFAFYNGEWDLAQKALDDIIYRAQLELYPEPLLVANAIKASLPHGPMKSNKEGTRC
IQVEITPT

Primary citation

Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA. Suresh, S., Shaw, A.L., Akintola, D.K. et al. J Biol Chem (2025) 301:110886-110886. DOI 10.1016/j.jbc.2025.110886 · PubMed

Other PDB entries of the same protein (UniProt P42356 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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