EMDB-0601: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug...

Basic information

• Entry: Database: EMDB / ID: EMD-0601
• Title: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with PP tRNA
• Sample: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with PP tRNA

Function / homology

Function:

Vif-mediated degradation of APOBEC3G / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Selenocysteine synthesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / Oxidative Stress Induced Senescence / Integrin cell surface interactions / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH1 Intracellular Domain Regulates Transcription / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of activated PAK-2p34 by proteasome mediated degradation / NF-kB is activated and signals survival / Resolution of Sister Chromatid Cohesion / Senescence-Associated Secretory Phenotype (SASP) / Cargo recognition for clathrin-mediated endocytosis / NOTCH2 Activation and Transmission of Signal to the Nucleus / Autodegradation of the E3 ubiquitin ligase COP1 / Glycogen synthesis / RMTs methylate histone arginines / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Regulation of innate immune responses to cytosolic DNA / Eukaryotic Translation Termination / Oncogene Induced Senescence / Ubiquitin-dependent degradation of Cyclin D / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD Domain Mutants / Stimuli-sensing channels / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Regulation of PLK1 Activity at G2/M Transition / p75NTR recruits signalling complexes / NRIF signals cell death from the nucleus / Deactivation of the beta-catenin transactivating complex / InlA-mediated entry of Listeria monocytogenes into host cells / APC/C:Cdc20 mediated degradation of Cyclin B / E3 ubiquitin ligases ubiquitinate target proteins / DDX58/IFIH1-mediated induction of interferon-alpha/beta / InlB-mediated entry of Listeria monocytogenes into host cell / TICAM1, RIP1-mediated IKK complex recruitment / NOD1/2 Signaling Pathway / mTORC1-mediated signalling / SCF-beta-TrCP mediated degradation of Emi1 / Budding and maturation of HIV virion / Peptide chain elongation / L13a-mediated translational silencing of Ceruloplasmin expression / Degradation of the extracellular matrix / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Stabilization of p53 / Spry regulation of FGF signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Downstream TCR signaling / EGFR downregulation / TCF dependent signaling in response to WNT / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Degradation of beta-catenin by the destruction complex / Clathrin-mediated endocytosis / Viral mRNA Translation / SCF(Skp2)-mediated degradation of p27/p21 / Downregulation of ERBB2 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vpu mediated degradation of CD4 / SRP-dependent cotranslational protein targeting to membrane / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Assembly Of The HIV Virion / Membrane binding and targetting of GAG proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Apoptotic cleavage of cell adhesion proteins / Myoclonic epilepsy of Lafora / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / Ovarian tumor domain proteases / Ub-specific processing proteases / UCH proteinases / Gap-filling DNA repair synthesis and ligation in GG-NER / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / HDR through Homologous Recombination (HRR) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translation initiation complex formation / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Negative regulation of MAPK pathway / Regulation of TP53 Activity through Methylation / Cyclin D associated events in G1 / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin / Mitotic Prometaphase

Domain/homology:

Ribosomal protein L11, conserved site / 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 / Cadherin prodomain / Ribosomal protein L23/L15e core domain superfamily / Cadherin-like superfamily / 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 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e/L16 / WD40-repeat-containing domain / Ribosomal protein L30, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L34e, conserved site / Ribosomal protein L41 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L13 / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L7, eukaryotic / Ribosomal protein S12/S23 / Ribosomal protein S30 / Ribosomal protein L34Ae / Ribosomal protein S13/S15, N-terminal / 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 / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L7Ae/L8/Nhp2 family / 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 L31e, conserved site / Ribosomal protein S6e, 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 L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal Proteins L2, C-terminal domain / Cadherin conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal S24e conserved site / Ribosomal protein L22/L17, 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 L29, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein S3, 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 S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L5, conserved site / Ribosomal protein L22/L17 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S26e / Ribosomal protein L11/L12 / 60S ribosomal protein L6E / Ribosomal protein L24e-related / Ribosomal protein L23/L25, conserved site

Component:

40S ribosomal protein S7 / 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 S13 / 60S ribosomal protein L7a / 40S ribosomal protein S11 / 60S ribosomal protein L30 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S15a / 40S ribosomal protein S28 / 60S ribosomal protein L32 / 60S ribosomal protein L39 / Receptor of activated protein C kinase 1 / Similar to ribosomal protein L23 / 60S ribosomal protein L18 / 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 L10a / 40S ribosomal protein S8 / 60S ribosomal protein L13 / 60S ribosomal protein L37 / 60S ribosomal protein L17 / 60S ribosomal protein L22 / 60S ribosomal protein L9 / 60S ribosomal protein L12 / 60S ribosomal protein L10 / 40S ribosomal protein S12 / 40S ribosomal protein S3 / 40S ribosomal protein S4, Y isoform 1 / 60S ribosomal protein L7 / 40S ribosomal protein S19 / 60S ribosomal protein L35a / 40S ribosomal protein S2 / Cadherin-1 / 40S ribosomal protein SA / 40S ribosomal protein S17 / 60S acidic ribosomal protein P0 / 40S ribosomal protein S30 / 60S ribosomal protein L4 / 60S ribosomal protein L3 / 60S ribosomal protein L37a / 60S ribosomal protein L29 / 60S ribosomal protein L27 / 60S ribosomal protein L15 / 60S ribosomal protein L26 / 40S ribosomal protein S3a / 40S ribosomal protein S20 / 60S ribosomal protein L14 / 60S ribosomal protein L34 / 40S ribosomal protein S10 / 60S ribosomal protein L13a / 40S ribosomal protein S5 / 40S ribosomal protein S9 / 60S ribosomal protein L28 / 60S ribosomal protein L21 / 60S ribosomal protein L5 / 60S ribosomal protein L27a / 60S ribosomal protein L35 / 40S ribosomal protein S27 / 60S ribosomal protein L36

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.4 Å
• Authors: Li W / Cate JHD

Funding support

3 items

Organization	Grant number	Country

• 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: 6olg; ; SummaryFull reportAbout validation report

History

Deposition	Feb 21, 2019	-
Header (metadata) release	Mar 20, 2019	-
Map release	Mar 20, 2019	-
Update	Jun 19, 2019	-
Current status	Jun 19, 2019	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_0601.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.15 Å

Density

Contour Level	By EMDB: 0.02 / Movie #1: 0.02
Minimum - Maximum	-0.05380252 - 0.10746834
Average (Standard dev.)	0.00044285491 (±0.006211472)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 410 410 410 Spacing 410 410 410
Cell	A=B=C: 471.5 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	410	410	410
origin x/y/z	0.000	0.000	0.000
length x/y/z	471.500	471.500	471.500
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	410	410	410
D min/max/mean	-0.054	0.107	0.000

Supplemental data

Sample components

Entire Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug...

• Entire: Name: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with PP tRNA; Number of components: 1

Component #1: protein, Human ribosome nascent chain complex (CDH1-RNC) stalled ...

• Protein: Name: Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with PP tRNA; 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

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.8
• Support film: unspecified
• Vitrification: Cryogen name: ETHANE / Temperature: 277 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: 50 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 / Applied symmetry: C₁ (asymmetric) / Number of projections: 16594
• 3D reconstruction: Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

• Modeling #1: Refinement space: REAL / Overall bvalue: 62

Output model

6olg