EMDB-0599: Structure of a drug-like molecule stalled CDH1 ribosome nascent c...

Basic information

• Entry: Database: EMDB / ID: EMD-0599
• Title: Structure of a drug-like molecule stalled CDH1 ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA
• Map data: PF846 stalled human ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA;map is sharpened.

Sample

• Complex: human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA tRNA and PE tRNA

Function / homology

Function:

response to heparin / desmosome assembly / pituitary gland development / response to Gram-positive bacterium / gamma-catenin binding / desmosome / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / Regulation of CDH1 mRNA translation by microRNAs / cellular response to lithium ion / cellular response to indole-3-methanol / cell adhesion mediator activity / calcium-dependent cell-cell adhesion / adherens junction organization / cell-cell adhesion mediated by cadherin / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / flotillin complex / Developmental Lineage of Mammary Stem Cells / Formation of definitive endoderm / embryonic brain development / Apoptotic cleavage of cell adhesion proteins / catenin complex / translation at presynapse / response to insecticide / Regulation of CDH1 Function / cell-cell junction assembly / regulation of translation involved in cellular response to UV / Adherens junctions interactions / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / negative regulation of cell-cell adhesion / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / GTPase activating protein binding / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / G1 to G0 transition / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of ubiquitin-protein transferase activity / GAIT complex / nucleolus organization / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / negative regulation of DNA repair / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / ankyrin binding / erythrocyte homeostasis / supercoiled DNA binding / regulation of establishment of cell polarity / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / NF-kappaB complex / apical junction complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / homophilic cell-cell adhesion / negative regulation of myoblast fusion / ion channel inhibitor activity / positive regulation of mitochondrial depolarization / Developmental Lineage of Mammary Gland Myoepithelial Cells / protein kinase A binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / TOR signaling / BH3 domain binding / negative regulation of translational frameshifting / iron-sulfur cluster binding / monocyte chemotaxis / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / gastrulation / regulation of cell division / lateral plasma membrane / protein localization to nucleus / positive regulation of GTPase activity

Domain/homology:

Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / 40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / : / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L6e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family

Component:

FAU ubiquitin like and ribosomal protein S30 fusion / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Cadherin-1 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL36

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.9 Å
• Authors: Li W / Cate JHD

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Human Genome Research Institute	R01-GM065050	United States

• 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.

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_0599.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: PF846 stalled human ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA;map is sharpened.
• Voxel size: X=Y=Z: 1.15 Å

Density

Contour Level	By AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum	-0.04674063 - 0.09558096
Average (Standard dev.)	0.00046730065 (±0.005918665)

• 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	-0.047	0.096	0.000

Supplemental data

Additional map: PF846 stalled human ribosome nascent chain complex (CDH1-RNC)...

• File: emd_0599_additional.map
• Annotation: PF846 stalled human ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA;map is not sharpened.

Half map: Half map of PF846 stalled human ribosome nascent...

• File: emd_0599_half_map_1.map
• Annotation: Half map of PF846 stalled human ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA.

Half map: Half map of PF846 stalled human ribosome nascent...

• File: emd_0599_half_map_2.map
• Annotation: Half map of PF846 stalled human ribosome nascent chain complex (CDH1-RNC) in rotated state with AA tRNA and PE tRNA.

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 AA tRNA and PE tRNA

Components

• Complex: human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA tRNA and PE tRNA

Supramolecule #1: human ribosome nascent chain complex (CDH1-RNC) stalled by a drug...

• Supramolecule: Name: human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA tRNA and PE tRNA; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Homo sapiens (human) / Recombinant cell: HeLa
• Molecular weight: Theoretical: 4.3 MDa

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.8
• Grid: Details: unspecified
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10350
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION

Atomic model buiding 1

• Refinement: Space: REAL / Overall B value: 73

Output model

PDB-6olf:
Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs