+Open data
-Basic information
Entry | Database: PDB / ID: 6bq1 | ||||||
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Title | Human PI4KIIIa lipid kinase complex | ||||||
Components |
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Keywords | Transferase/Signaling Protein / kinase / phosphoinositide synthesis / Transferase-Signaling Protein complex | ||||||
Function / homology | Function and homology information : / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / viral replication complex formation and maintenance / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling ...: / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / viral replication complex formation and maintenance / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / Golgi-associated vesicle membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / myelination / protein localization to plasma membrane / kinase activity / cadherin binding / neuron projection / phosphorylation / viral RNA genome replication / focal adhesion / signal transduction / extracellular exosome / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Lees, J.A. / Zhang, Y. / Oh, M. / Schauder, C.M. / Yu, X. / Baskin, J. / Dobbs, K. / Notarangelo, L.D. / Camilli, P.D. / Walz, T. / Reinisch, K.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bq1.cif.gz | 821.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bq1.ent.gz | 649.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bq1_validation.pdf.gz | 1003.4 KB | Display | wwPDB validaton report |
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Full document | 6bq1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6bq1_validation.xml.gz | 142 KB | Display | |
Data in CIF | 6bq1_validation.cif.gz | 216.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/6bq1 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bq1 | HTTPS FTP |
-Related structure data
Related structure data | 7129MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 173821.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KA, PIK4, PIK4CA / Production host: Homo sapiens (human) References: UniProt: P42356, 1-phosphatidylinositol 4-kinase | ||||||||||
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#2: Protein | Mass: 96460.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTC7B, TTC7L1 / Production host: Homo sapiens (human) / References: UniProt: Q86TV6 #3: Protein | Mass: 32688.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM126A, DRCTNNB1A / Production host: Homo sapiens (human) / References: UniProt: Q9BYI3 #4: Protein | | Mass: 173906.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KA, PIK4, PIK4CA / Production host: Homo sapiens (human) References: UniProt: P42356, 1-phosphatidylinositol 4-kinase #5: Chemical | Compound details | The sequence or connectivity could be assigned to the N-terminal residues of Entity-1 (PI4KA). They ...The sequence or connectivity could be assigned to the N-terminal residues of Entity-1 (PI4KA). They have been modeled as UNK residues | Sequence details | The actual sequence of the N-terminal region modeled as UNK is: ...The actual sequence of the N-terminal region modeled as UNK is: MDYKDHDGDY | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human phosphatidylinositol 4-kinase III alpha complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.7 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293F | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38461 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3280 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Particle selection | Num. of particles selected: 508504 | ||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64104 / Symmetry type: POINT |