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- EMDB-44382: Structure of the PI4KA complex bound to Calcineurin -

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Basic information

Entry
Database: EMDB / ID: EMD-44382
TitleStructure of the PI4KA complex bound to Calcineurin
Map dataPI4KIIIa lipid kinase complex bound to Calcineurin cryo EM - Map
Sample
  • Complex: PI4KA complex bound to Calcineurin
    • Protein or peptide: Phosphatidylinositol 4-kinase alpha
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Hyccin
    • Protein or peptide: Calcineurin subunit B type 1
    • Protein or peptide: Protein phosphatase 3 catalytic subunit alpha
  • Ligand: CALCIUM ION
KeywordsPI4KIIIa complex / PI4KA / TTC7B / FAM126A / CNA / CNB / Calcineurin / SIGNALING PROTEIN
Function / homology
Function and homology information


reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / 1-phosphatidylinositol 4-kinase ...reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / positive regulation of saliva secretion / Schwann cell migration / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / renal filtration / lung epithelial cell differentiation / Synthesis of PIPs at the Golgi membrane / calcineurin-NFAT signaling cascade / modulation by host of viral process / Golgi-associated vesicle membrane / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / skeletal muscle tissue regeneration / transition between fast and slow fiber / phosphatidylinositol biosynthetic process / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / extrinsic component of plasma membrane / dendrite morphogenesis / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine phosphatase activity / branching involved in blood vessel morphogenesis / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatidylinositol-mediated signaling / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / phosphatidylinositol phosphate biosynthetic process / positive regulation of activated T cell proliferation / calcineurin-mediated signaling / positive regulation of endocytosis / Calcineurin activates NFAT / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / multicellular organismal response to stress / phosphatase binding / negative regulation of insulin secretion / skeletal muscle fiber development / keratinocyte differentiation / protein dephosphorylation / myelination / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of cell adhesion / hippocampal mossy fiber to CA3 synapse / T cell activation / protein localization to plasma membrane / excitatory postsynaptic potential / wound healing / modulation of chemical synaptic transmission / cellular response to glucose stimulus / sarcolemma / Schaffer collateral - CA1 synapse / Z disc / G1/S transition of mitotic cell cycle / response to calcium ion / protein import into nucleus / calcium ion transport / heart development / ATPase binding / actin cytoskeleton organization / Ca2+ pathway / dendritic spine / postsynapse / calmodulin binding / neuron projection / protein dimerization activity / positive regulation of cell migration / cadherin binding
Similarity search - Function
PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : / PP2B, metallophosphatase domain / PP2B / Anaphase-promoting complex, cyclosome, subunit 3 ...PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : / PP2B, metallophosphatase domain / PP2B / Anaphase-promoting complex, cyclosome, subunit 3 / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Tetratricopeptide repeat / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase alpha / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha / Tetratricopeptide repeat protein 7B / Hyccin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShaw AL / Suresh S / Yip CK / Burke JE
Funding support Canada, 2 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)NSERC-2020-04241 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-03951 Canada
CitationJournal: Structure / Year: 2024
Title: Structure of calcineurin bound to PI4KA reveals dual interface in both PI4KA and FAM126A.
Authors: Alexandria L Shaw / Sushant Suresh / Matthew A H Parson / Noah J Harris / Meredith L Jenkins / Calvin K Yip / John E Burke /
Abstract: Phosphatidylinositol 4-kinase alpha (PI4KA) maintains the phosphatidylinositol 4-phosphate (PI4P) and phosphatidylserine pools of the plasma membrane. A key regulator of PI4KA is its association into ...Phosphatidylinositol 4-kinase alpha (PI4KA) maintains the phosphatidylinositol 4-phosphate (PI4P) and phosphatidylserine pools of the plasma membrane. A key regulator of PI4KA is its association into a complex with TTC7 and FAM126 proteins. This complex can be regulated by the CNAβ1 isoform of the phosphatase calcineurin. We previously identified that CNAβ1 directly binds to FAM126A. Here, we report a cryoelectron microscopic (cryo-EM) structure of a truncated PI4KA complex bound to calcineurin, revealing a unique direct interaction between PI4KA and calcineurin. Hydrogen deuterium exchange mass spectrometry (HDX-MS) and computational analysis show that calcineurin forms a complex with an evolutionarily conserved IKISVT sequence in PI4KA's horn domain. We also characterized conserved LTLT and PSISIT calcineurin binding sequences in the C terminus of FAM126A. These dual sites in PI4KA and FAM126A are both in close proximity to phosphorylation sites in the PI4KA complex, suggesting key roles of calcineurin-regulated phosphosites in PI4KA regulation. This work reveals novel insight into how calcineurin can regulate PI4KA activity.
History
DepositionApr 2, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44382.png

Downloads & links

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Map

FileDownload / File: emd_44382.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPI4KIIIa lipid kinase complex bound to Calcineurin cryo EM - Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 520 pix.
= 415.8 Å		0.8 Å/pix.
x 520 pix.
= 415.8 Å		0.8 Å/pix.
x 520 pix.
= 415.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79962 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.53840786 - 1.5263281
Average (Standard dev.)0.0018805559 (±0.038318586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 415.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PI4KA complex bound to Calcineurin

EntireName: PI4KA complex bound to Calcineurin
Components
  • Complex: PI4KA complex bound to Calcineurin
    • Protein or peptide: Phosphatidylinositol 4-kinase alpha
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Hyccin
    • Protein or peptide: Calcineurin subunit B type 1
    • Protein or peptide: Protein phosphatase 3 catalytic subunit alpha
  • Ligand: CALCIUM ION

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Supramolecule #1: PI4KA complex bound to Calcineurin

SupramoleculeName: PI4KA complex bound to Calcineurin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: Stabilized with BS3 crosslinker
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Phosphatidylinositol 4-kinase alpha

MacromoleculeName: Phosphatidylinositol 4-kinase alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 237.102281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAPARGGG GGGGGGGGCS GSGSSASRGF YFNTVLSLAR SLAVQRPASL EKVQKLLCMC PVDFHGIFQL DERRRDAVIA LGIFLIESD LQHKDCVVPY LLRLLKGLPK VYWVEESTAR KGRGALPVAE SFSFCLVTLL SDVAYRDPSL RDEILEVLLQ V LHVLLGMC ...String:
MAAAPARGGG GGGGGGGGCS GSGSSASRGF YFNTVLSLAR SLAVQRPASL EKVQKLLCMC PVDFHGIFQL DERRRDAVIA LGIFLIESD LQHKDCVVPY LLRLLKGLPK VYWVEESTAR KGRGALPVAE SFSFCLVTLL SDVAYRDPSL RDEILEVLLQ V LHVLLGMC QALEIQDKEY LCKYAIPCLI GISRAFGRYS NMEESLLSKL FPKIPPHSLR VLEELEGVRR RSFNDFRSIL PS NLLTVCQ EGTLKRKTSS VSSISQVSPE RGMPPPSSPG GSAFHYFEAS CLPDGTALEP EYYFSTISSS FSVSPLFNGV TYK EFNIPL EMLRELLNLV KKIVEEAVLK SLDAIVASVM EANPSADLYY TSFSDPLYLT MFKMLRDTLY YMKDLPTSFV KEIH DFVLE QFNTSQGELQ KILHDADRIH NELSPLKLRC QANAACVDLM VWAVKDEQGA ENLCIKLSEK LQSKTSSKVI IAHLP LLIC CLQGLGRLCE RFPVVVHSVT PSLRDFLVIP SPVLVKLYKY HSQYHTVAGN DIKISVTNEH SESTLNVMSG KKSQPS MYE QLRDIAIDNI CRCLKAGLTV DPVIVEAFLA SLSNRLYISQ ESDKDAHLIP DHTIRALGHI AVALRDTPKV MEPILQI LQ QKFCQPPSPL DVLIIDQLGC LVITGNQYIY QEVWNLFQQI SVKASSVVYS ATKDYKDHGY RHCSLAVINA LANIAANI Q DEHLVDELLM NLLELFVQLG LEGKRASERA SEKGPALKAS SSAGNLGVLI PVIAVLTRRL PPIKEAKPRL QKLFRDFWL YSVLMGFAVE GSGLWPEEWY EGVCEIATKS PLLTFPSKEP LRSVLQYNSA MKNDTVTPAE LSELRSTIIN LLDPPPEVSA LINKLDFAM STYLLSVYRL EYMRVLRSTD PDRFQVMFCY FEDKAIQKDK SGMMQCVIAV ADKVFDAFLN MMADKAKTKE N EEELERHA QFLLVNFNHI HKRIRRVADK YLSGLVDKFP HLLWSGTVLK TMLDILQTLS LSLSADIHKD QPYYDIPDAP YR ITVPDTY EARESIVKDF AARCGMILQE AMKWAPTVTK SHLQEYLNKH QNWVSGLSQH TGLAMATESI LHFAGYNKQN TTL GATQLS ERPACVKKDY SNFMASLNLR NRYAGEVYGM IRFSGTTGQM SDLNKMMVQD LHSALDRSHP QHYTQAMFKL TAML ISSKD CDPQLLHHLC WGPLRMFNEH GMETALACWE WLLAGKDGVE VPFMREMAGA WHMTVEQKFG LFSAEIKEAD PLAAS EASQ PKPCPPEVTP HYIWIDFLVQ RFEIAKYCSS DQVEIFSSLL QRSMSLNIGG AKGSMNRHVA AIGPRFKLLT LGLSLL HAD VVPNATIRNV LREKIYSTAF DYFSCPPKFP TQGEKRLRED ISIMIKFWTA MFSDKKYLTA SQLVPPDNQD TRSNLDI TV GSRQQATQGW INTYPLSSGM STISKKSGMS KKTNRGSQLH KYYMKRRTLL LSLLATEIER LITWYNPLSA PELELDQA G ENSVANWRSK YISLSEKQWK DNVNLAWSIS PYLAVQLPAR FKNTEAIGNE VTRLVRLDPG AVSDVPEAIK FLVTWHTID ADAPELSHVL CWAPTDPPTG LSYFSSMYPP HPLTAQYGVK VLRSFPPDAI LFYIPQIVQA LRYDKMGYVR EYILWAASKS QLLAHQFIW NMKTNIYLDE EGHQKDPDIG DLLDQLVEEI TGSLSGPAKD FYQREFDFFN KITNVSAIIK PYPKGDERKK A CLSALSEV KVQPGCYLPS NPEAIVLDID YKSGTPMQSA AKAPYLAKFK VKRCGVSELE KEGLRCRSDS EDECSTQEAD GQ KISWQAA IFKVGDDCRQ DMLALQIIDL FKNIFQLVGL DLFVFPYRVV ATAPGCGVIE CIPDCTSRDQ LGRQTDFGMY DYF TRQYGD ESTLAFQQAR YNFIRSMAAY SLLLFLLQIK DRHNGNIMLD KKGHIIHIDF GFMFESSPGG NLGWEPDIKL TDEM VMIMG GKMEATPFKW FMEMCVRGYL AVRPYMDAVV SLVTLMLDTG LPCFRGQTIK LLKHRFSPNM TEREAANFIM KVIQS CFLS NRSRTYDMIQ YYQNDIPY

UniProtKB: Phosphatidylinositol 4-kinase alpha

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Macromolecule #2: Tetratricopeptide repeat protein 7B

MacromoleculeName: Tetratricopeptide repeat protein 7B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.294109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPRG PKPQLTEVRK HLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR VIAEAYATKG LCLEKLPISS S TSNLHVDR ...String:
MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPRG PKPQLTEVRK HLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR VIAEAYATKG LCLEKLPISS S TSNLHVDR EQDVITCYEK AGDIALLYLQ EIERVILSNI QNRSPKPGPA PHDQELGFFL ETGLQRAHVL YFKNGNLTRG VG RFRELLR AVETRTTQNL RMTIARQLAE ILLRGMCEQS YWNPLEDPPC QSPLDDPLRK GANTKTYTLT RRARVYSGEN IFC PQENTE EALLLLLISE SMANRDAVLS RIPEHKSDRL ISLQSASVVY DLLTIALGRR GQYEMLSECL ERAMKFAFEE FHLW YQFAL SLMAAGKSAR AVKVLKECIR LKPDDATIPL LAAKLCMGSL HWLEEAEKFA KTVVDVGEKT SEFKAKGYLA LGLTY SLQA TDASLRGMQE VLQRKALLAF QRAHSLSPTD HQAAFYLALQ LAISRQIPEA LGYVRQALQL QGDDANSLHL LALLLS AQK HYHDALNIID MALSEYPENF ILLFSKVKLQ SLCRGPDEAL LTCKHMLQIW KSCYNLTNPS DSGRGSSLLD RTIADRR QL NTITLPDFSD PETGSVHATS VAASRVEQAL SEVASSLQSS APKQGPLHPW MTLAQIWLHA AEVYIGIGKP AEATACTQ E AANLFPMSHN VLYMRGQIAE LRGSMDEARR WYEEALAISP THVKSMQRLA LILHQLGRYS LAEKILRDAV QVNSTAHEV WNGLGEVLQA QGNDAAATEC FLTALELEAS SPAVPFTIIP RVL

UniProtKB: Tetratricopeptide repeat protein 7B

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Macromolecule #3: Hyccin

MacromoleculeName: Hyccin / type: protein_or_peptide / ID: 3 / Details: Truncated construct (1-308) / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.638867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFTSEKGVVE EWLSEFKTLP ETSLPNYATN LKDKSSLVSS LYKVIQEPQS ELLEPVCHQL FEFYRSGEEQ LLQFTLQFLP ELIWCYLAV SASRNVHSSG CIEALLLGVY NLEIVDKQGH TKVLSFTIPS LSKPSVYHEP SSIGSMALTE SALSQHGLSK V VYSGPHPQ ...String:
MFTSEKGVVE EWLSEFKTLP ETSLPNYATN LKDKSSLVSS LYKVIQEPQS ELLEPVCHQL FEFYRSGEEQ LLQFTLQFLP ELIWCYLAV SASRNVHSSG CIEALLLGVY NLEIVDKQGH TKVLSFTIPS LSKPSVYHEP SSIGSMALTE SALSQHGLSK V VYSGPHPQ REMLTAQNRF EVLTFLLLCY NAALTYMPSV SLQSLCQICS RICVCGYPRQ HVRKYKGISS RIPVSSGFMV QM LTGIYFA FYNGEWDLAQ KALDDIIYRA QLELYPEPLL VANAIKASLP HGPMKSNKEG TRCIQVEITP T

UniProtKB: Hyccin

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Macromolecule #4: Calcineurin subunit B type 1

MacromoleculeName: Calcineurin subunit B type 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.322904 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGNEASYPLE MCSHFDADEI KRLGKRFKKL DLDNSGSLSV EEFMSLPELQ QNPLVQRVID IFDTDGNGEV DFKEFIEGVS QFSVKGDKE QKLRFAFRIY DMDKDGYISN GELFQVLKMM VGNNLKDTQL QQIVDKTIIN ADKDGDGRIS FEEFCAVVGG L DIHKKMVV DV

UniProtKB: Calcineurin subunit B type 1

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Macromolecule #5: Protein phosphatase 3 catalytic subunit alpha

MacromoleculeName: Protein phosphatase 3 catalytic subunit alpha / type: protein_or_peptide / ID: 5
Details: Truncated Calcineurin A alpha (2-391) L236P D238N,Truncated Calcineurin A alpha (2-391) L236P D238N
Number of copies: 2 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.883242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SEPKAIDPKL STTDRVVKAV PFPPSHRLTA KEVFDNDGKP RVDILKAHLM KEGRLEESVA LRIITEGASI LRQEKNLLDI DAPVTVCGD IHGQFFDLMK LFEVGGSPAN TRYLFLGDYV DRGYFSIECV LYLWALKILY PKTLFLLRGN HECRHLTEYF T FKQECKIK ...String:
SEPKAIDPKL STTDRVVKAV PFPPSHRLTA KEVFDNDGKP RVDILKAHLM KEGRLEESVA LRIITEGASI LRQEKNLLDI DAPVTVCGD IHGQFFDLMK LFEVGGSPAN TRYLFLGDYV DRGYFSIECV LYLWALKILY PKTLFLLRGN HECRHLTEYF T FKQECKIK YSERVYDACM DAFDCLPLAA LMNQQFLCVH GGLSPEINTL DDIRKLDRFK EPPAYGPMCD ILWSDPPENF GN EKTQEHF THNTVRGCSY FYSYPAVCEF LQHNNLLSIL RAHEAQDAGY RMYRKSQTTG FPSLITIFSA PNYLDVYNNK AAV LKYENN VMNIRQFNCS PHPYWLPNFM DVFTWSLPFV GEKVTEMLVN VLNICSDDEL GSEEDGFDGA TAAAFKQECK IKYS ERVYD ACMDAFDCLP LAALMNQQFL CVHGGLSPEI NTLDDIRKLD RFKEPPAYGP MCDILWSDPP EDFGNEKTQE HFTHN TVRG CSYFYSYPAV CEFLQHNNLL SILRAHEAQD AGYRMYRKSQ TTGFPSLITI FSAPNYLDVY NNKAAVLKYE NNVMNI RQF NCSPHPYWLP NFMDVFTWSL PFVGEKVTEM LVNVLNICSD DELGSEEDGF DGATAAA

UniProtKB: Protein phosphatase 3 catalytic subunit alpha, Protein phosphatase 3 catalytic subunit alpha

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration0.77 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC3H4N2Imidazole
150.0 mMNaClSodium Chloride
5.0 %C3H8O3Glycerol
0.5 mMTCEPTris(2-carboxyethyl)phosphine

Details: Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
Details: Glow discharged using the Pelco EasiGlow. 15mA Current.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -5, blot time 1 s.
DetailsSample was treated with BS3 crosslinker then gel filtered to isolate protein peak consistent with a dimer of pentamers.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 10121 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1181312
Details: Particles were picked using the cryoSPARC template picker
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio with 2 classes
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235760
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1) / Details: CryoSPARC SGD-based ab intio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1) / Details: CryoSPARC - Non-Uniform Refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6bq1

source_name: PDB, initial_model_type: experimental model

6nuc

source_name: PDB, initial_model_type: experimental model
Output model

PDB-9b9g:
Structure of the PI4KA complex bound to Calcineurin

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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