EMDB-0526: Structure of drug-like molecule stalled USO1 ribosome nascent cha...

Basic information

• Entry: Database: EMDB / ID: EMD-0526
• Title: Structure of drug-like molecule stalled USO1 ribosome nascent chain complex (human)
• Sample: Drug-like molecule PF846 stalled human ribosome nascent chain complex, USO1-RNC:; nucleic-acidNucleic acid

Function / homology

Function:

N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / Pink/Parkin Mediated Mitophagy / Degradation of GLI2 by the proteasome / Regulation of FZD by ubiquitination / 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 / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Circadian Clock / 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 / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / ABC-family proteins mediated transport / MAPK6/MAPK4 signaling / NRIF signals cell death from the nucleus / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / Downstream TCR signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Selenocysteine synthesis / Myoclonic epilepsy of Lafora / FCERI mediated NF-kB activation / Deactivation of the beta-catenin transactivating complex / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Separation of Sister Chromatids / Stimuli-sensing channels / 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 / HDR through Homologous Recombination (HRR) / UCH proteinases / SRP-dependent cotranslational protein targeting to membrane / 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 / Antigen processing: Ubiquitination & Proteasome degradation

Domain/homology:

Ribosomal protein L2, conserved site / Ribosomal S11, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / WD40-repeat-containing domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal protein S2, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L19/L19e, domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L35Ae, conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13-like, H2TH / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L2, domain 3 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L32e, conserved site / Ribosomal protein L37e, conserved site / K homology domain superfamily, prokaryotic type / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / G-protein beta WD-40 repeat / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein S15P / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L39e, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L31e, conserved site / WD40 repeat, conserved site / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ubiquitin / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / S15/NS1, RNA-binding / Translation protein, beta-barrel domain superfamily / Ribosomal protein L13, conserved site / WD40 repeat / Ribosomal protein S19e / Ribosomal protein S3, C-terminal / Ribosomal protein S6e / Ribosomal protein L13e / Ribosomal protein L32e / Ribosomal protein L37e / Ribosomal protein S3Ae / Ribosomal protein L35A / Ribosomal protein S14 / Ribosomal protein S10 / Ribosomal protein L29/L35 / Ribosomal protein S2 / Ribosomal protein S13

Component:

60S ribosomal protein L23a / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S23 / 40S ribosomal protein S4, X isoform / 60S ribosomal protein L7a / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / 40S ribosomal protein S14 / 60S ribosomal protein L30 / 40S ribosomal protein S28 / 60S ribosomal protein L18 / 60S ribosomal protein L39 / Receptor of activated protein C kinase 1 / Similar to ribosomal protein L23 / 40S ribosomal protein S15a / 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 S16 / 60S ribosomal protein L5 / 40S ribosomal protein S8 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 60S ribosomal protein L4 / 60S ribosomal protein L22 / 60S ribosomal protein L9 / 60S ribosomal protein L10 / 60S ribosomal protein L13 / 40S ribosomal protein S3 / 60S ribosomal protein L13a / 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 S30 / 60S ribosomal protein L3 / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 60S ribosomal protein L14 / 60S ribosomal protein L37 / 60S ribosomal protein L37a / 60S ribosomal protein L27 / 60S ribosomal protein L15 / 60S ribosomal protein L26 / 40S ribosomal protein S3a / 40S ribosomal protein S20 / 60S ribosomal protein L34 / 60S ribosomal protein L35 / 60S ribosomal protein L29 / 40S ribosomal protein S10 / 40S ribosomal protein S5 / 40S ribosomal protein S9 / 60S ribosomal protein L28 / 60S ribosomal protein L21 / 60S ribosomal protein L27a / 60S ribosomal protein L36

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Li W / Cate JHD
• Citation: Journal: Nat. Struct. Mol. Biol. / Year: 2019; Title: Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.; Authors: Wenfei Li / Fred R Ward / Kim F McClure / Stacey Tsai-Lan Chang / Elizabeth Montabana / Spiros Liras / Robert G Dullea / Jamie H D Cate / ; Abstract: The drug-like molecule PF-06446846 (PF846) binds the human ribosome and selectively blocks the translation of a small number of proteins by an unknown mechanism. In structures of PF846-stalled human ribosome nascent chain complexes, PF846 binds in the ribosome exit tunnel in a eukaryotic-specific pocket formed by 28S ribosomal RNA, and alters the path of the nascent polypeptide chain. PF846 arrests the translating ribosome in the rotated state of translocation, in which the peptidyl-transfer RNA 3'-CCA end is improperly docked in the peptidyl transferase center. Selections of messenger RNAs from mRNA libraries using translation extracts reveal that PF846 can stall translation elongation, arrest termination or even enhance translation, depending on nascent chain sequence context. These results illuminate how a small molecule selectively targets translation by the human ribosome, and provides a foundation for developing small molecules that modulate the production of proteins of therapeutic interest.
• Validation Report: PDB-ID: 6oli; ; SummaryFull reportAbout validation report
• Date: Deposition: Feb 6, 2019 / Header (metadata) release: Mar 6, 2019 / Map release: Jun 5, 2019 / Update: Jun 19, 2019

Map

• File: Download / File: emd_0526.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.15 Å

Density

Contour Level	By AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum	-0.052317448 - 0.10637717
Average (Standard dev.)	0.00046923864 (±0.0061468002)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 460.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.15	1.15	1.15
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	460.000	460.000	460.000
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	400	400	400
D min/max/mean	-0.052	0.106	0.000

Supplemental data

Sample components

Entire Drug-like molecule PF846 stalled human ribosome nascent chain com...

• Entire: Name: Drug-like molecule PF846 stalled human ribosome nascent chain complex, USO1-RNC; Number of components: 2

Component #1: protein, Drug-like molecule PF846 stalled human ribosome nascent ...

• Protein: Name: Drug-like molecule PF846 stalled human ribosome nascent chain complex, USO1-RNC; Recombinant expression: No
• Mass: Theoretical: 4.3 MDa
• Source: Species: Homo sapiens (human)
• Source (engineered): Expression System: Homo sapiens (human) / Cell of expression system: HeLa

Component #2: nucleic-acid, Drug-like molecule PF846 stalled human ribosome nas...

nucleic acid

Name: Drug-like molecule PF846 stalled human ribosome nascent chain complex, USO1-RNC
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

RMKPWFEVGD ENSGWSAQKV TNLHLMLQLV RVLVSPTNPP GA

• Source: Species: Homo sapiens (human)

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.8
• Support film: unspecified
• Vitrification: Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 55 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: OTHER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image processing

• Processing: Method: single particle reconstruction / Number of projections: 38314
• 3D reconstruction: Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

• Modeling #1: Refinement space: REAL / Overall bvalue: 91

Output model

6oli