EMDB-9699: Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure i)

Basic information

• Entry: Database: EMDB / ID: EMD-9699
• Title: Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure i)
• Sample: Human 80S ribosome

Function / homology

Function:

Pink/Parkin Mediated Mitophagy / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / TNFR1-induced NFkappaB signaling pathway / Regulation of TNFR1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of FZD by ubiquitination / Degradation of GLI2 by the proteasome / Degradation of DVL / Degradation of AXIN / Asymmetric localization of PCP proteins / AUF1 (hnRNP D0) binds and destabilizes mRNA / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Regulation of RAS by GAPs / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / Regulation of necroptotic cell death / Negative regulation of MAPK pathway / TNFR2 non-canonical NF-kB pathway / RHO GTPases Activate Formins / Termination of translesion DNA synthesis / TNFR1-mediated ceramide production / Translesion synthesis by POLI / Translesion synthesis by POLK / Negative regulation of FGFR4 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR1 signaling / Hedgehog 'on' state / Circadian Clock / Myoclonic epilepsy of Lafora / MAPK6/MAPK4 signaling / Downregulation of TGF-beta receptor signaling / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH1 Intracellular Domain Regulates Transcription / Regulation of activated PAK-2p34 by proteasome mediated degradation / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / NRIF signals cell death from the nucleus / Downstream TCR signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Viral mRNA Translation / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Deactivation of the beta-catenin transactivating complex / Constitutive Signaling by NOTCH1 HD Domain Mutants / Autodegradation of the E3 ubiquitin ligase COP1 / Glycogen synthesis / RMTs methylate histone arginines / Regulation of innate immune responses to cytosolic DNA / NOTCH2 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Stimuli-sensing channels / Selenocysteine synthesis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Regulation of PLK1 Activity at G2/M Transition / Oncogene Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / HDR through Homologous Recombination (HRR) / UCH proteinases / APC-Cdc20 mediated degradation of Nek2A / Regulation of RUNX3 expression and activity / TICAM1-dependent activation of IRF3/IRF7 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of expression of SLITs and ROBOs / ER Quality Control Compartment (ERQC) / Neddylation / Regulation of PTEN stability and activity / Regulation of PTEN localization / Regulation of RUNX2 expression and activity / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Protein methylation / InlA-mediated entry of Listeria monocytogenes into host cells / InlB-mediated entry of Listeria monocytogenes into host cell / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Downregulation of ERBB2 signaling / TICAM1,TRAF6-dependent induction of TAK1 complex / Peroxisomal protein import / Cargo recognition for clathrin-mediated endocytosis / Negative regulation of NOTCH4 signaling

Domain/homology:

Ribosomal protein S19 conserved site / Ribosomal protein L10e/L16 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / WD40-repeat-containing domain / Ribosomal protein S4e, central region / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, N-terminal / Ribosomal protein L10e, conserved site / TRASH domain / Ribosomal protein S30 / Ribosomal protein L41 / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Ribosomal protein L37ae/L37e / Ribosomal protein S5, N-terminal / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L29, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L7, eukaryotic / Ribosomal protein L15e, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L14P, conserved site / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S17, conserved site / Ubiquitin / Ribosomal protein L21e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S19e, conserved site / Ubiquitin conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein S12/S23 / Ribosomal protein L24/L26, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L13e / Ribosomal protein L21e / Ribosomal protein L15, conserved site / Ribosomal protein L10e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S3, C-terminal / Ribosomal protein S6e / Ribosomal protein L32e / Ribosomal protein L22/L17 / Ribosomal protein L37e

Component:

40S ribosomal protein S6 / 40S ribosomal protein S28 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / 60S ribosomal protein L23 / 40S ribosomal protein S29 / 60S ribosomal protein L23a / 40S ribosomal protein S4, X isoform / Eukaryotic peptide chain release factor subunit 1 / 60S ribosomal protein L7a / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S18 / 60S ribosomal protein L30 / 40S ribosomal protein S30 / 60S ribosomal protein L18 / 60S ribosomal protein L39 / Receptor of activated protein C kinase 1 / 60S ribosomal protein L10-like / 40S ribosomal protein S14 / 60S ribosomal protein L6 / 60S ribosomal protein L18a / 60S ribosomal protein L19 / 60S ribosomal protein L36a / 60S ribosomal protein L24 / 40S ribosomal protein S21 / 60S ribosomal protein L31 / 60S ribosomal protein L38 / Ubiquitin-60S ribosomal protein L40 / Ubiquitin-40S ribosomal protein S27a / 60S ribosomal protein L41 / 60S ribosomal protein L8 / 60S ribosomal protein L11 / 60S ribosomal protein L32 / 40S ribosomal protein S23 / 40S ribosomal protein S9 / 40S ribosomal protein S16 / 60S ribosomal protein L13 / 60S ribosomal protein L13a / 60S ribosomal protein L3 / 40S ribosomal protein S19 / 60S ribosomal protein L4 / 60S ribosomal protein L22 / 60S ribosomal protein L9 / 40S ribosomal protein S12 / 60S ribosomal protein L35 / 40S ribosomal protein S3 / 60S ribosomal protein L17 / 60S ribosomal protein L7 / 60S ribosomal protein L35a / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S17 / 40S ribosomal protein S27 / 60S ribosomal protein L27a / 40S ribosomal protein S15a / 40S ribosomal protein S3a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 60S ribosomal protein L37 / 60S ribosomal protein L37a / 60S ribosomal protein L27 / 60S ribosomal protein L15 / 60S ribosomal protein L26 / 40S ribosomal protein S20 / 60S ribosomal protein L5 / 60S ribosomal protein L14 / 60S ribosomal protein L34 / 60S ribosomal protein L29 / 40S ribosomal protein S10 / 40S ribosomal protein S5 / 60S ribosomal protein L28 / 60S ribosomal protein L21 / 60S ribosomal protein L36

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 4.5 Å
• Authors: Yokohama T / Shigematsu H / Shirouzu M / Imataka H / Ito T
• Citation: Journal: Mol. Cell / Year: 2019; Title: HCV IRES Captures an Actively Translating 80S Ribosome.; Authors: Takeshi Yokoyama / Kodai Machida / Wakana Iwasaki / Tomoaki Shigeta / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Yoshie Harada / Hideki Shigematsu / Mikako Shirouzu / Hisashi Tadakuma / Hiroaki Imataka / Takuhiro Ito / ; Abstract: Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to the solvent side of the 40S platform of the cap-dependently translating 80S ribosome. Furthermore, we obtained the cryo-EM structures of the HCV IRES capturing the 40S subunit of the IRES-dependently translating 80S ribosome. In the elucidated structures, the HCV IRES "body," consisting of domain III except for subdomain IIIb, binds to the 40S subunit, while the "long arm," consisting of domain II, remains flexible and does not impede the ongoing translation. Biochemical experiments revealed that the cap-dependently translating ribosome becomes a better substrate for the HCV IRES than the free ribosome. Therefore, the HCV IRES is likely to efficiently induce the translation initiation of its downstream mRNA with the captured translating ribosome as soon as the ongoing translation terminates.
• Validation Report: PDB-ID: 6ip8; ; SummaryFull reportAbout validation report
• Date: Deposition: Nov 2, 2018 / Header (metadata) release: May 29, 2019 / Map release: May 29, 2019 / Update: May 29, 2019

Map

• File: Download / File: emd_9699.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.49 Å

Density

Contour Level	By AUTHOR: 0.0375 / Movie #1: 0.05
Minimum - Maximum	-0.15732701 - 0.25015217
Average (Standard dev.)	0.00030095442 (±0.012908177)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 420 420 420 Spacing 420 420 420
Cell	A=B=C: 625.8 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.49	1.49	1.49
M x/y/z	420	420	420
origin x/y/z	0.000	0.000	0.000
length x/y/z	625.800	625.800	625.800
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	420	420	420
D min/max/mean	-0.157	0.250	0.000

Supplemental data

Sample components

Entire Human 80S ribosome

• Entire: Name: Human 80S ribosome / Number of components: 1

Component #1: protein, Human 80S ribosome

• Protein: Name: Human 80S ribosome / Recombinant expression: No
• Source: Species: Homo sapiens (human)

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.5
• Vitrification: Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

• Experimental equipment: Model: Talos Arctica / Image courtesy: FEI Company
• Imaging: Microscope: FEI TECNAI ARCTICA
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Magnification: 23500.0 X (nominal), 33557.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: OTHER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image processing

• Processing: Method: single particle reconstruction / Applied symmetry: C₁ (asymmetric) / Number of projections: 27869
• 3D reconstruction: Software: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

6ip8