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- EMDB-7129: Human PI4KIIIa lipid kinase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-7129
TitleHuman PI4KIIIa lipid kinase complex
Map dataHuman PI4KIIIa lipid kinase complex
Sample
  • Complex: Human phosphatidylinositol 4-kinase III alpha complex
    • Protein or peptide: Phosphatidylinositol 4-kinase III alpha (PI4KA)
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Protein FAM126A
    • Protein or peptide: Phosphatidylinositol 4-kinase III alpha (PI4KA)
  • Ligand: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide
Keywordskinase / phosphoinositide synthesis / Transferase-Signaling Protein complex
Function / homology
Function and homology information


reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process ...reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / phosphorylation / myelination / protein localization to plasma membrane / kinase activity / neuron projection / cadherin binding / focal adhesion / signal transduction / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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 / : / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Phosphoinositide 3-kinase family, accessory domain (PIK domain) ...PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / 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. / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase alpha / Tetratricopeptide repeat protein 7B / Hyccin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLees JA / Zhang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114068 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Architecture of the human PI4KIIIα lipid kinase complex.
Authors: Joshua A Lees / Yixiao Zhang / Michael S Oh / Curtis M Schauder / Xiaoling Yu / Jeremy M Baskin / Kerry Dobbs / Luigi D Notarangelo / Pietro De Camilli / Thomas Walz / Karin M Reinisch /
Abstract: Plasma membrane (PM) phosphoinositides play essential roles in cell physiology, serving as both markers of membrane identity and signaling molecules central to the cell's interaction with its ...Plasma membrane (PM) phosphoinositides play essential roles in cell physiology, serving as both markers of membrane identity and signaling molecules central to the cell's interaction with its environment. The first step in PM phosphoinositide synthesis is the conversion of phosphatidylinositol (PI) to PI4P, the precursor of PI(4,5)P and PI(3,4,5)P This conversion is catalyzed by the PI4KIIIα complex, comprising a lipid kinase, PI4KIIIα, and two regulatory subunits, TTC7 and FAM126. We here report the structure of this complex at 3.6-Å resolution, determined by cryo-electron microscopy. The proteins form an obligate ∼700-kDa superassembly with a broad surface suitable for membrane interaction, toward which the kinase active sites are oriented. The structural complexity of the assembly highlights PI4P synthesis as a major regulatory junction in PM phosphoinositide homeostasis. Our studies provide a framework for further exploring the mechanisms underlying PM phosphoinositide regulation.
History
DepositionNov 27, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseDec 13, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bq1
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7129.png

Downloads & links

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Map

FileDownload / File: emd_7129.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman PI4KIIIa lipid kinase complex
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.16651683 - 0.2872219
Average (Standard dev.)0.00042148505 (±0.0058580837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1670.2870.000

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Supplemental data

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Sample components

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Entire : Human phosphatidylinositol 4-kinase III alpha complex

EntireName: Human phosphatidylinositol 4-kinase III alpha complex
Components
  • Complex: Human phosphatidylinositol 4-kinase III alpha complex
    • Protein or peptide: Phosphatidylinositol 4-kinase III alpha (PI4KA)
    • Protein or peptide: Tetratricopeptide repeat protein 7B
    • Protein or peptide: Protein FAM126A
    • Protein or peptide: Phosphatidylinositol 4-kinase III alpha (PI4KA)
  • Ligand: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide

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Supramolecule #1: Human phosphatidylinositol 4-kinase III alpha complex

SupramoleculeName: Human phosphatidylinositol 4-kinase III alpha complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Phosphatidylinositol 4-kinase III alpha (PI4KA)

MacromoleculeName: Phosphatidylinositol 4-kinase III alpha (PI4KA) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173.821438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MMQCV IAVADKVFDA FLNMM ADKA KTKENEEELE RHAQFLLVNF NHIHKRIRRV ADKYLSGLVD KFPHLLWSGT VLKTMLDILQ TLSLSLSADI HKDQPY YDI PDAPYRITVP DTYEARESIV KDFAARCGMI LQEAMKWAPT VTKSHLQEYL NKHQNWVSGL SQHTGLAMAT ESILHFA GY NKQNTTLGAT QLSERPACVK KDYSNFMASL NLRNRYAGEV YGMIRFSGTT GQMSDLNKMM VQDLHSALDR SHPQHYTQ A MFKLTAMLIS SKDCDPQLLH HLCWGPLRMF NEHGMETALA CWEWLLAGKD GVEVPFMREM AGAWHMTVEQ KFGLFSAEI KEADPLAASE ASQPKPCPPE VTPHYIWIDF LVQRFEIAKY CSSDQVEIFS SLLQRSMSLN IGGAKGSMNR HVAAIGPRFK LLTLGLSLL HADVVPNATI RNVLREKIYS TAFDYFSCPP KFPTQGEKRL REDISIMIKF WTAMFSDKKY LTASQLVPPD N QDTRSNLD ITVGSRQQAT QGWINTYPLS SGMSTISKKS GMSKKTNRGS QLHKYYMKRR TLLLSLLATE IERLITWYNP LS APELELD QAGENSVANW RSKYISLSEK QWKDNVNLAW SISPYLAVQL PARFKNTEAI GNEVTRLVRL DPGAVSDVPE AIK FLVTWH TIDADAPELS HVLCWAPTDP PTGLSYFSSM YPPHPLTAQY GVKVLRSFPP DAILFYIPQI VQALRYDKMG YVRE YILWA ASKSQLLAHQ FIWNMKTNIY LDEEGHQKDP DIGDLLDQLV EEITGSLSGP AKDFYQREFD FFNKITNVSA IIKPY PKGD ERKKACLSAL SEVKVQPGCY LPSNPEAIVL DIDYKSGTPM QSAAKAPYLA KFKVKRCGVS ELEKEGLRCR SDSEDE CST QEADGQKISW QAAIFKVGDD CRQDMLALQI IDLFKNIFQL VGLDLFVFPY RVVATAPGCG VIECIPDCTS RDQLGRQ TD FGMYDYFTRQ YGDESTLAFQ QARYNFIRSM AAYSLLLFLL QIKDRHNGNI MLDKKGHIIH IDFGFMFESS PGGNLGWE P DIKLTDEMVM IMGGKMEATP FKWFMEMCVR GYLAVRPYMD AVVSLVTLML DTGLPCFRGQ TIKLLKHRFS PNMTEREAA NFIMKVIQSC FLSNRSRTYD MIQYYQNDIP Y

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: 96.46057 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYPYDVPDYA AIAGAPDLKL MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPR GPKPQLTEVR KHLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR V IAEAYATK ...String:
MYPYDVPDYA AIAGAPDLKL MATKKAGSRL ETEIERCRSE CQWERIPELV KQLSAKLIAN DDMAELLLGE SKLEQYLKEH PLRQGASPR GPKPQLTEVR KHLTAALDRG NLKSEFLQES NLIMAKLNYV EGDYKEALNI YARVGLDDLP LTAVPPYRLR V IAEAYATK GLCLEKLPIS SSTSNLHVDR EQDVITCYEK AGDIALLYLQ EIERVILSNI QNRSPKPGPA PHDQELGFFL ET GLQRAHV LYFKNGNLTR GVGRFRELLR AVETRTTQNL RMTIARQLAE ILLRGMCEQS YWNPLEDPPC QSPLDDPLRK GAN TKTYTL TRRARVYSGE NIFCPQENTE EALLLLLISE SMANRDAVLS RIPEHKSDRL ISLQSASVVY DLLTIALGRR GQYE MLSEC LERAMKFAFE EFHLWYQFAL SLMAAGKSAR AVKVLKECIR LKPDDATIPL LAAKLCMGSL HWLEEAEKFA KTVVD VGEK TSEFKAKGYL ALGLTYSLQA TDASLRGMQE VLQRKALLAF QRAHSLSPTD HQAAFYLALQ LAISRQIPEA LGYVRQ ALQ LQGDDANSLH LLALLLSAQK HYHDALNIID MALSEYPENF ILLFSKVKLQ SLCRGPDEAL LTCKHMLQIW KSCYNLT NP SDSGRGSSLL DRTIADRRQL NTITLPDFSD PETGSVHATS VAASRVEQAL SEVASSLQSS APKQGPLHPW MTLAQIWL H AAEVYIGIGK PAEATACTQE AANLFPMSHN VLYMRGQIAE LRGSMDEARR WYEEALAISP THVKSMQRLA LILHQLGRY SLAEKILRDA VQVNSTAHEV WNGLGEVLQA QGNDAAATEC FLTALELEAS SPAVPFTIIP RVL

UniProtKB: Tetratricopeptide repeat protein 7B

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Macromolecule #3: Protein FAM126A

MacromoleculeName: Protein FAM126A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.688514 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGSFTSEKG VVEEWLSEFK TLPETSLPNY ATNLKDKSSL VSSLYKVIQE PQSELLEPVC HQLFEFYRSG EEQLLQFTLQ FLPELIWCY LAVSASRNVH SSGCIEALLL GVYNLEIVDK QGHTKVLSFT IPSLSKPSVY HEPSSIGSMA LTESALSQHG L SKVVYSGP ...String:
GPGSFTSEKG VVEEWLSEFK TLPETSLPNY ATNLKDKSSL VSSLYKVIQE PQSELLEPVC HQLFEFYRSG EEQLLQFTLQ FLPELIWCY LAVSASRNVH SSGCIEALLL GVYNLEIVDK QGHTKVLSFT IPSLSKPSVY HEPSSIGSMA LTESALSQHG L SKVVYSGP HPQREMLTAQ NRFEVLTFLL LCYNAALTYM PSVSLQSLCQ ICSRICVCGY PRQHVRKYKG ISSRIPVSSG FM VQMLTGI YFAFYNGEWD LAQKALDDII YRAQLELYPE PLLVANAIKA SLPHG

UniProtKB: Hyccin

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Macromolecule #4: Phosphatidylinositol 4-kinase III alpha (PI4KA)

MacromoleculeName: Phosphatidylinositol 4-kinase III alpha (PI4KA) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol 4-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173.906547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)MMQC VIAVADKVFD A FLNMMADK AKTKENEEEL ERHAQFLLVN FNHIHKRIRR VADKYLSGLV DKFPHLLWSG TVLKTMLDIL QTLSLSLSAD IH KDQPYYD IPDAPYRITV PDTYEARESI VKDFAARCGM ILQEAMKWAP TVTKSHLQEY LNKHQNWVSG LSQHTGLAMA TES ILHFAG YNKQNTTLGA TQLSERPACV KKDYSNFMAS LNLRNRYAGE VYGMIRFSGT TGQMSDLNKM MVQDLHSALD RSHP QHYTQ AMFKLTAMLI SSKDCDPQLL HHLCWGPLRM FNEHGMETAL ACWEWLLAGK DGVEVPFMRE MAGAWHMTVE QKFGL FSAE IKEADPLAAS EASQPKPCPP EVTPHYIWID FLVQRFEIAK YCSSDQVEIF SSLLQRSMSL NIGGAKGSMN RHVAAI GPR FKLLTLGLSL LHADVVPNAT IRNVLREKIY STAFDYFSCP PKFPTQGEKR LREDISIMIK FWTAMFSDKK YLTASQL VP PDNQDTRSNL DITVGSRQQA TQGWINTYPL SSGMSTISKK SGMSKKTNRG SQLHKYYMKR RTLLLSLLAT EIERLITW Y NPLSAPELEL DQAGENSVAN WRSKYISLSE KQWKDNVNLA WSISPYLAVQ LPARFKNTEA IGNEVTRLVR LDPGAVSDV PEAIKFLVTW HTIDADAPEL SHVLCWAPTD PPTGLSYFSS MYPPHPLTAQ YGVKVLRSFP PDAILFYIPQ IVQALRYDKM GYVREYILW AASKSQLLAH QFIWNMKTNI YLDEEGHQKD PDIGDLLDQL VEEITGSLSG PAKDFYQREF DFFNKITNVS A IIKPYPKG DERKKACLSA LSEVKVQPGC YLPSNPEAIV LDIDYKSGTP MQSAAKAPYL AKFKVKRCGV SELEKEGLRC RS DSEDECS TQEADGQKIS WQAAIFKVGD DCRQDMLALQ IIDLFKNIFQ LVGLDLFVFP YRVVATAPGC GVIECIPDCT SRD QLGRQT DFGMYDYFTR QYGDESTLAF QQARYNFIRS MAAYSLLLFL LQIKDRHNGN IMLDKKGHII HIDFGFMFES SPGG NLGWE PDIKLTDEMV MIMGGKMEAT PFKWFMEMCV RGYLAVRPYM DAVVSLVTLM LDTGLPCFRG QTIKLLKHRF SPNMT EREA ANFIMKVIQS CFLSNRSRTY DMIQYYQNDI PY

UniProtKB: Phosphatidylinositol 4-kinase alpha

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Macromolecule #5: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(...

MacromoleculeName: 5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide
type: ligand / ID: 5 / Number of copies: 2 / Formula: E4S
Molecular weightTheoretical: 574.626 Da
Chemical component information

ChemComp-E4S:
5-{2-amino-1-[4-(morpholin-4-yl)phenyl]-1H-benzimidazol-6-yl}-N-(2-fluorophenyl)-2-methoxypyridine-3-sulfonamide

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
200.0 mMSodium chlorideNaCl
5.0 %Glycerol
1.0 mMTCEP-HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number real images: 3280 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.7 µm / Calibrated defocus min: 1.8 µm / Calibrated magnification: 38461 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 22500
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: 508504
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 64104
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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