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- EMDB-12534: Structure of the yeast Gcn1 bound to a leading stalled 80S riboso... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12534 | |||||||||
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Title | Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A | |||||||||
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Function / homology | ![]() positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pochopien AA / Beckert B / Wilson DN | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Authors: Agnieszka A Pochopien / Bertrand Beckert / Sergo Kasvandik / Otto Berninghausen / Roland Beckmann / Tanel Tenson / Daniel N Wilson / ![]() ![]() Abstract: The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for ...The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation. The fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, a negative regulator of Gcn2. Despite the wealth of available biochemical data, information on structures of Gcn proteins on the ribosome has remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the P-stalk and the A-site region of the lead ribosome. The lead ribosome is stalled in a nonrotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, and Rbg2/Gir2 in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site, and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings reveal the interaction mode of the Gcn2-activating protein Gcn1 with colliding ribosomes and provide insight into the regulation of Gcn2 activation. The binding of Gcn1 to a disome has important implications not only for the Gcn2-activated ISR, but also for the general ribosome-associated quality control pathways. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 689.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 113.4 KB 113.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.8 KB | Display | ![]() |
Images | ![]() | 248 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 265.7 MB 265.6 MB 1 GB 98.2 MB 265.8 MB 265.7 MB 1 GB 687.9 MB 1 GB 1 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nrcMC ![]() 7nrdC 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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Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Additional map: #1
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+Additional map: #8
+Half map: #1
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Sample components
+Entire : Structure of the yeast Gcn1-bound leading stalled 80S ribosome wi...
+Supramolecule #1: Structure of the yeast Gcn1-bound leading stalled 80S ribosome wi...
+Macromolecule #1: 18S rRNA (1771-MER)
+Macromolecule #2: RNA (5'-R(P*AP*UP*GP*AP*AP*A)-3')
+Macromolecule #36: tRNA (76-MER)
+Macromolecule #37: tRNA (75-MER)
+Macromolecule #40: 25S rRNA (3184-MER)
+Macromolecule #41: 5S rRNA (121-MER)
+Macromolecule #42: 5.8S rRNA (158-MER)
+Macromolecule #3: 40S ribosomal protein S0-A
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S15
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S3
+Macromolecule #8: 40S ribosomal protein S4-A
+Macromolecule #9: 40S ribosomal protein S5
+Macromolecule #10: 40S ribosomal protein S6-A
+Macromolecule #11: 40S ribosomal protein S7-A
+Macromolecule #12: 40S ribosomal protein S8-A
+Macromolecule #13: 40S ribosomal protein S9-A
+Macromolecule #14: 40S ribosomal protein S10-A
+Macromolecule #15: 40S ribosomal protein S11-A
+Macromolecule #16: 40S ribosomal protein S12
+Macromolecule #17: 40S ribosomal protein S13
+Macromolecule #18: 40S ribosomal protein S14-B
+Macromolecule #19: 40S ribosomal protein S16-A
+Macromolecule #20: 40S ribosomal protein S17-B
+Macromolecule #21: 40S ribosomal protein S18-A
+Macromolecule #22: 40S ribosomal protein S19-A
+Macromolecule #23: 40S ribosomal protein S20
+Macromolecule #24: 40S ribosomal protein S21-A
+Macromolecule #25: 40S ribosomal protein S22-A
+Macromolecule #26: 40S ribosomal protein S23-A
+Macromolecule #27: 40S ribosomal protein S24-A
+Macromolecule #28: 40S ribosomal protein S25-A
+Macromolecule #29: 40S ribosomal protein S26-B
+Macromolecule #30: 40S ribosomal protein S27-A
+Macromolecule #31: 40S ribosomal protein S29-A
+Macromolecule #32: 40S ribosomal protein S30-A
+Macromolecule #33: 40S ribosomal protein S31
+Macromolecule #34: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #35: 40S ribosomal protein S28-A
+Macromolecule #38: Ribosome-interacting GTPase 2
+Macromolecule #39: GIR2
+Macromolecule #43: 60S ribosomal protein L2-A
+Macromolecule #44: 60S ribosomal protein L3
+Macromolecule #45: 60S ribosomal protein L4-A
+Macromolecule #46: 60S ribosomal protein L5
+Macromolecule #47: 60S ribosomal protein L6-B
+Macromolecule #48: 60S ribosomal protein L7-A
+Macromolecule #49: 60S ribosomal protein L8-A
+Macromolecule #50: 60S ribosomal protein L9-A
+Macromolecule #51: 60S ribosomal protein L10
+Macromolecule #52: 60S ribosomal protein L11-B
+Macromolecule #53: 60S ribosomal protein L13-A
+Macromolecule #54: 60S ribosomal protein L14-A
+Macromolecule #55: 60S ribosomal protein L15-A
+Macromolecule #56: 60S ribosomal protein L16-A
+Macromolecule #57: 60S ribosomal protein L17-A
+Macromolecule #58: 60S ribosomal protein L18-A
+Macromolecule #59: 60S ribosomal protein L19-A
+Macromolecule #60: 60S ribosomal protein L20-A
+Macromolecule #61: 60S ribosomal protein L21-A
+Macromolecule #62: 60S ribosomal protein L22-A
+Macromolecule #63: 60S ribosomal protein L23-A
+Macromolecule #64: 60S ribosomal protein L24-A
+Macromolecule #65: 60S ribosomal protein L25
+Macromolecule #66: 60S ribosomal protein L26-A
+Macromolecule #67: 60S ribosomal protein L27-A
+Macromolecule #68: 60S ribosomal protein L28
+Macromolecule #69: 60S ribosomal protein L29
+Macromolecule #70: 60S ribosomal protein L30
+Macromolecule #71: 60S ribosomal protein L31-A
+Macromolecule #72: 60S ribosomal protein L32
+Macromolecule #73: 60S ribosomal protein L33-A
+Macromolecule #74: 60S ribosomal protein L34-A
+Macromolecule #75: 60S ribosomal protein L35-A
+Macromolecule #76: 60S ribosomal protein L36-A
+Macromolecule #77: 60S ribosomal protein L37-A
+Macromolecule #78: 60S ribosomal protein L38
+Macromolecule #79: 60S ribosomal protein L39
+Macromolecule #80: 60S ribosomal protein L40-A
+Macromolecule #81: 60S ribosomal protein L41-A
+Macromolecule #82: 60S ribosomal protein L42-A
+Macromolecule #83: 60S ribosomal protein L43-A
+Macromolecule #84: eiF5A
+Macromolecule #85: L1 60S ribosomal protein
+Macromolecule #86: GCN1
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |