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- EMDB-50125: Mammalian quaternary complex of a translating 80S ribosome, NAC, ... -
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Open data
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Basic information
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Title | Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E | ||||||||||||||||||
![]() | homogeneously refined cryo-EM map of the quaternary RNC-NAC-NatA/E-MetAP1 complex | ||||||||||||||||||
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![]() | translation / ribosome / NAC / N-terminal acetyltransferase / NatA / NatE / MetAP1 | ||||||||||||||||||
Function / homology | ![]() negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / 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 / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / 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 / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / skeletal muscle tissue regeneration / initiator methionyl aminopeptidase activity / histone H4 acetyltransferase activity / heart trabecula morphogenesis / establishment of mitotic sister chromatid cohesion / methionyl aminopeptidase / negative regulation of formation of translation preinitiation complex / metalloexopeptidase activity / N-acetyltransferase activity / GAIT complex / regulation of G1 to G0 transition / laminin receptor activity / 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 / mitotic sister chromatid cohesion / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / homeostatic process / internal protein amino acid acetylation / protein acetylation / activation-induced cell death of T cells / macrophage chemotaxis / lung morphogenesis / metalloaminopeptidase activity / positive regulation of signal transduction by p53 class mediator / glutathione transferase / phagocytic cup / ubiquitin ligase inhibitor activity / protein maturation / glutathione transferase activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chromosome organization / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / aminopeptidase activity / cytosolic ribosome / laminin binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / glutathione metabolic process / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / wound healing / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / cellular response to type II interferon / platelet aggregation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||||||||||||||
![]() | Yudin D / Scaiola A / Ban N | ||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: NAC guides a ribosomal multienzyme complex for nascent protein processing Authors: Lentzsch AM / Yudin D / Gamerdinger M / Chandrasekar S / Rabl L / Scaiola A / Deuerling E / Ban N / Shan S | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 336.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 136.7 KB 136.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21 KB | Display | ![]() |
Images | ![]() | 138.9 KB | ||
Masks | ![]() ![]() | 669.9 MB 669.9 MB | ![]() | |
Filedesc metadata | ![]() | 25.1 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 626.8 MB 625.5 MB 34 MB 621.6 MB 621.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f1cMC ![]() 9f1bC ![]() 9f1dC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | homogeneously refined cryo-EM map of the quaternary RNC-NAC-NatA/E-MetAP1 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Mask #2
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-Additional map: main map lowpass filtered to 6 A resolution
File | emd_50125_additional_1.map | ||||||||||||
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Annotation | main map lowpass filtered to 6 A resolution | ||||||||||||
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-Additional map: main map lowpass filtered to 8 A resolution
File | emd_50125_additional_2.map | ||||||||||||
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Annotation | main map lowpass filtered to 8 A resolution | ||||||||||||
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-Additional map: main map lowpass filtered to estimated local resolution
File | emd_50125_additional_3.map | ||||||||||||
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Annotation | main map lowpass filtered to estimated local resolution | ||||||||||||
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-Half map: halfmap A
File | emd_50125_half_map_1.map | ||||||||||||
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Annotation | halfmap A | ||||||||||||
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-Half map: halfmap B
File | emd_50125_half_map_2.map | ||||||||||||
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Annotation | halfmap B | ||||||||||||
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Sample components
+Entire : Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...
+Supramolecule #1: Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and...
+Supramolecule #2: Rabbit ribosome-nascent chain complex
+Supramolecule #3: NAC heterodimer
+Supramolecule #4: Human methionine aminopeptidase 1
+Supramolecule #5: Human NatA/E complex
+Supramolecule #6: Human NatA complex
+Supramolecule #7: Human NatE with a GST tag
+Macromolecule #1: mRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: P-site tRNA
+Macromolecule #6: 5.8S rRNA
+Macromolecule #20: 28S rRNA
+Macromolecule #64: 18S rRNA
+Macromolecule #2: 60S ribosomal protein L29
+Macromolecule #5: 40S ribosomal protein S18
+Macromolecule #7: 60S ribosomal protein L22
+Macromolecule #8: 40S ribosomal protein S19
+Macromolecule #9: Large ribosomal subunit protein uL2
+Macromolecule #10: Ribosomal protein L23
+Macromolecule #11: Small ribosomal subunit protein uS10
+Macromolecule #12: Ribosomal protein L3
+Macromolecule #13: Large ribosomal subunit protein uL23
+Macromolecule #14: Small ribosomal subunit protein eS21
+Macromolecule #15: 60S ribosomal protein L4
+Macromolecule #16: Large ribosomal subunit protein uL22
+Macromolecule #17: 60S ribosomal protein L27
+Macromolecule #18: 40S ribosomal protein S23
+Macromolecule #19: 60S ribosomal protein L6
+Macromolecule #21: Large ribosomal subunit protein eL18
+Macromolecule #22: 60S ribosomal protein L27a
+Macromolecule #23: 40S ribosomal protein S24
+Macromolecule #24: Ribosomal Protein uL30
+Macromolecule #25: Ribosomal protein L26
+Macromolecule #26: Ribosomal protein L24
+Macromolecule #27: 40S ribosomal protein SA
+Macromolecule #28: 40S ribosomal protein S25
+Macromolecule #29: 60S ribosomal protein L7a
+Macromolecule #30: Ribosomal protein S15a
+Macromolecule #31: Ribosomal protein L19
+Macromolecule #32: 40S ribosomal protein S3a
+Macromolecule #33: 60S ribosomal protein L41
+Macromolecule #34: 60S ribosomal protein L9
+Macromolecule #35: Large ribosomal subunit protein eL20
+Macromolecule #36: Small ribosomal subunit protein uS5
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: 60S ribosomal protein L10
+Macromolecule #39: Large ribosomal subunit protein uL18
+Macromolecule #40: Methionine aminopeptidase 1
+Macromolecule #41: 40S ribosomal protein S3
+Macromolecule #42: 60S ribosomal protein L31
+Macromolecule #43: 60S ribosomal protein L11
+Macromolecule #44: Nascent polypeptide-associated complex subunit alpha
+Macromolecule #45: 40S ribosomal protein S4
+Macromolecule #46: Ribosomal protein L32
+Macromolecule #47: Nascent chain
+Macromolecule #48: Transcription factor BTF3
+Macromolecule #49: Ribosomal protein S5
+Macromolecule #50: 60S ribosomal protein L35a
+Macromolecule #51: Large ribosomal subunit protein eL13
+Macromolecule #52: Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetylt...
+Macromolecule #53: 40S ribosomal protein S6
+Macromolecule #54: 60S ribosomal protein L34
+Macromolecule #55: 60S ribosomal protein L14
+Macromolecule #56: N-alpha-acetyltransferase 15, NatA auxiliary subunit
+Macromolecule #57: 40S ribosomal protein S7
+Macromolecule #58: 60S ribosomal protein L35
+Macromolecule #59: Ribosomal protein L15
+Macromolecule #60: N-alpha-acetyltransferase 10
+Macromolecule #61: 40S ribosomal protein S8
+Macromolecule #62: 60S ribosomal protein L36
+Macromolecule #63: Large ribosomal subunit protein uL13
+Macromolecule #65: 40S ribosomal protein S9
+Macromolecule #66: Ribosomal protein L37
+Macromolecule #67: 40S ribosomal protein S27
+Macromolecule #68: S10_plectin domain-containing protein
+Macromolecule #69: 60S ribosomal protein L38
+Macromolecule #70: 40S ribosomal protein S28
+Macromolecule #71: 40S ribosomal protein S11
+Macromolecule #72: 60S ribosomal protein L39-like
+Macromolecule #73: Ribosomal protein S27a
+Macromolecule #74: 40S ribosomal protein S12
+Macromolecule #75: Large ribosomal subunit protein eL40
+Macromolecule #76: 40S ribosomal protein S30
+Macromolecule #77: 40S ribosomal protein S13
+Macromolecule #78: Large ribosomal subunit protein eL42
+Macromolecule #79: Small ribosomal subunit protein eS26
+Macromolecule #80: Small ribosomal subunit protein uS11
+Macromolecule #81: 60S ribosomal protein L37a
+Macromolecule #82: Small ribosomal subunit protein RACK1
+Macromolecule #83: 40S ribosomal protein uS19
+Macromolecule #84: 60S ribosomal protein L28
+Macromolecule #85: 40S ribosomal protein S29
+Macromolecule #86: Small ribosomal subunit protein uS9
+Macromolecule #87: Large ribosomal subunit protein uL10
+Macromolecule #88: 60S ribosomal protein L21
+Macromolecule #89: 40S ribosomal protein eS17
+Macromolecule #90: 60S ribosomal protein L12
+Macromolecule #91: UNKNOWN ATOM OR ION
+Macromolecule #92: MAGNESIUM ION
+Macromolecule #93: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #94: SPERMIDINE
+Macromolecule #95: SPERMINE
+Macromolecule #96: ZINC ION
+Macromolecule #97: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #98: water
-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: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: OTHER / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |