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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-14191 | |||||||||
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Title | Ternary complex of ribosome nascent chain with SRP and NAC | |||||||||
![]() | Ternary ribosome-nascent chain, SRP and NAC complex | |||||||||
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![]() | Ribosome / SRP / NAC / nascent chain / co-translational / Endoplasmic reticulum / co-translational protein targeting / co-translational folding | |||||||||
Function / homology | ![]() PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / Negative regulation of FLT3 / FLT3 signaling through SRC family kinases / RAF/MAP kinase cascade / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process ...PI3K Cascade / PIP3 activates AKT signaling / FLT3 Signaling / Negative regulation of FLT3 / FLT3 signaling through SRC family kinases / RAF/MAP kinase cascade / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / positive regulation of cell proliferation involved in heart morphogenesis / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / signal recognition particle, endoplasmic reticulum targeting / positive regulation of skeletal muscle tissue growth / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / cardiac ventricle development / granulocyte differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / signal recognition particle binding / signal recognition particle / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / skeletal muscle tissue regeneration / heart trabecula morphogenesis / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to membrane / regulation of G1 to G0 transition / embryonic hemopoiesis / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / G1 to G0 transition / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / cellular response to actinomycin D / ribonucleoprotein complex binding / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / neutrophil chemotaxis / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cytokine activity / positive regulation of translation / wound healing / cellular response to gamma radiation / receptor tyrosine kinase binding / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / GDP binding / unfolded protein binding / protein transport / retina development in camera-type eye / regulation of translation / 5S rRNA binding / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / in utero embryonic development / killing of cells of another organism / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / transcription coactivator activity / postsynaptic density / nuclear body / protein stabilization / rRNA binding / ribosome / nuclear speck / structural constituent of ribosome / ribonucleoprotein complex / response to xenobiotic stimulus / translation / protein domain specific binding / focal adhesion / GTPase activity / mRNA binding / ubiquitin protein ligase binding / synapse / positive regulation of cell population proliferation / positive regulation of gene expression Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
![]() | Jomaa A / Gamerdinger M / Hsieh H / Wallisch A / Chandrasekaran V / Ulusoy Z / Scaiola A / Hegde R / Shan S / Ban N / Deuerling E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting. Authors: Ahmad Jomaa / Martin Gamerdinger / Hao-Hsuan Hsieh / Annalena Wallisch / Viswanathan Chandrasekaran / Zeynel Ulusoy / Alain Scaiola / Ramanujan S Hegde / Shu-Ou Shan / Nenad Ban / Elke Deuerling / ![]() ![]() ![]() ![]() Abstract: The nascent polypeptide-associated complex (NAC) interacts with newly synthesized proteins at the ribosomal tunnel exit and competes with the signal recognition particle (SRP) to prevent mistargeting ...The nascent polypeptide-associated complex (NAC) interacts with newly synthesized proteins at the ribosomal tunnel exit and competes with the signal recognition particle (SRP) to prevent mistargeting of cytosolic and mitochondrial polypeptides to the endoplasmic reticulum (ER). How NAC antagonizes SRP and how this is overcome by ER targeting signals are unknown. Here, we found that NAC uses two domains with opposing effects to control SRP access. The core globular domain prevented SRP from binding to signal-less ribosomes, whereas a flexibly attached domain transiently captured SRP to permit scanning of nascent chains. The emergence of an ER-targeting signal destabilized NAC's globular domain and facilitated SRP access to the nascent chain. These findings elucidate how NAC hands over the signal sequence to SRP and imparts specificity of protein localization. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 321.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 78.7 KB 78.7 KB | Display Display | ![]() |
Images | ![]() | 173.5 KB | ||
Filedesc metadata | ![]() | 16.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 782.4 KB | Display | ![]() |
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Full document | ![]() | 782 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qwqMC ![]() 7qwrC ![]() 7qwsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ternary ribosome-nascent chain, SRP and NAC complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Ternary ribosome-nascent chain SRP NAC complex
+Supramolecule #1: Ternary ribosome-nascent chain SRP NAC complex
+Supramolecule #2: Ribosome
+Supramolecule #3: SRP RNA 7SL
+Supramolecule #4: Signal recognition particle proteins
+Supramolecule #5: Nascent chain preprolactin
+Supramolecule #6: Isoform 2 of Transcription factor BTF3
+Macromolecule #1: SRP RNA 7SL
+Macromolecule #9: 28S rRNA
+Macromolecule #47: 5S ribosomal RNA
+Macromolecule #49: 5.8S ribosomal RNA
+Macromolecule #2: Signal recognition particle 19 kDa protein
+Macromolecule #3: Nascent chain preprolactin
+Macromolecule #4: Isoform 2 of Transcription factor BTF3
+Macromolecule #5: Signal recognition particle subunit SRP68
+Macromolecule #6: Signal recognition particle 54 kDa protein
+Macromolecule #7: L8
+Macromolecule #8: 60S ribosomal protein L29
+Macromolecule #10: uL3
+Macromolecule #11: 60S ribosomal protein L30
+Macromolecule #12: 60S ribosomal protein L4
+Macromolecule #13: Ribosomal protein L31
+Macromolecule #14: Ribosomal_L18_c domain-containing protein
+Macromolecule #15: Ribosomal protein L32
+Macromolecule #16: 60S ribosomal protein L6
+Macromolecule #17: 60S ribosomal protein L35a
+Macromolecule #18: uL30
+Macromolecule #19: 60S ribosomal protein L34
+Macromolecule #20: 60S ribosomal protein L7a
+Macromolecule #21: 60S ribosomal protein L35
+Macromolecule #22: 60S ribosomal protein L9
+Macromolecule #23: 60S ribosomal protein L36
+Macromolecule #24: 60S ribosomal protein L10
+Macromolecule #25: Ribosomal protein L37
+Macromolecule #26: Ribosomal protein L11
+Macromolecule #27: 60S ribosomal protein L38
+Macromolecule #28: 60S ribosomal protein L13
+Macromolecule #29: Ribosomal protein L39
+Macromolecule #30: 60S ribosomal protein L14
+Macromolecule #31: Ubiquitin A-52 residue ribosomal protein fusion product 1
+Macromolecule #32: Ribosomal protein L15
+Macromolecule #33: 60s ribosomal protein l41
+Macromolecule #34: 60S ribosomal protein L13a
+Macromolecule #35: eL42
+Macromolecule #36: 60S ribosomal protein L17
+Macromolecule #37: eL43
+Macromolecule #38: eL18
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: 60S ribosomal protein L19
+Macromolecule #41: 60S ribosomal protein L18a
+Macromolecule #42: 60S ribosomal protein L21
+Macromolecule #43: Ribosomal protein L22
+Macromolecule #44: Ribosomal protein L23
+Macromolecule #45: Ribosomal protein L24
+Macromolecule #46: Ribosomal_L23eN domain-containing protein
+Macromolecule #48: Ribosomal protein L26
+Macromolecule #50: 60S ribosomal protein L27
+Macromolecule #51: 60S ribosomal protein L27a
+Macromolecule #52: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #53: MAGNESIUM ION
+Macromolecule #54: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen 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
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51843 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |