PDB-6oli: Structure of human ribosome nascent chain complex selectively sta...

ID or keywords:

Entry

Database: PDB / ID: 6oli

Title

Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)

Components

(40S ribosomal protein ...) x 32
(60S ribosomal protein ...) x 42
(tRNA) x 2
18S ribosomal RNA
28S ribosomal RNA
5.8S ribosomal RNA
5S ribosomal RNA
Nascent chain
Receptor of activated protein C kinase 1
mRNA

Keywords

RIBOSOME / selective stalling / drug-like molecule / human ribosome nascent chain complex

Function / homology

Function and homology information

eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / embryonic brain development ...eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / embryonic brain development / ribosomal protein import into nucleus / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / TORC2 complex binding / negative regulation of RNA splicing / negative regulation of DNA repair / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / A band / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / pigmentation / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / retinal ganglion cell axon guidance / mammalian oogenesis stage / fibroblast growth factor binding / homeostatic process / positive regulation of mitochondrial depolarization / G1 to G0 transition / activation-induced cell death of T cells / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / lung morphogenesis / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response
Similarity search - Function

40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S27e signature.
Similarity search - Domain/homology

Chem-MVM / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / FAU ubiquitin like and ribosomal protein S30 fusion / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 ...Chem-MVM / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / FAU ubiquitin like and ribosomal protein S30 fusion / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / 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
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å

Authors

Li, W. / Cate, J.H.D.

Funding support

United States, 1items

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 ...

History

Deposition	Apr 16, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Movie	Deposited structure unit Imaged by Jmol Download Superimposition on EM map EMDB-0526 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oli.cif.gz	4.6 MB	Display	PDBx/mmCIF format
PDB format	pdb6oli.ent.gz		Display	PDB format
PDBx/mmJSON format	6oli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oli_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6oli_full_validation.pdf.gz	1.9 MB	Display
Data in XML	6oli_validation.xml.gz	361.3 KB	Display
Data in CIF	6oli_validation.cif.gz	614.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ol/6oli ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6oli	HTTPS FTP

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Related structure data

Related structure data	0526MC 0596C 0597C 0598C 0599C 0600C 0601C 20134C 20135C 6oleC 6olfC 6olgC 6olzC 6om0C 6om7C M: map data used to model this data C: citing same article (ref.)
Similar structure data	6r6p-d 6om7-d 6om0-d 6mtc-d 5t2c-d 3221 6olf-d 6ip6-d 6hcq-d 9703 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (83) #10 - Oct 2000 Ribosome similarity (84) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (3) #260 - Aug 2021 Ribonuclease P similarity (8) #253 - Jan 2021 Expressome similarity (3) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #161 - May 2013 Ricin similarity (236) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #60 - Dec 2004 Ubiquitin similarity (83) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (115) #245 - May 2020 Spliceosomes similarity (3) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (79) #230 - Feb 2019 Initiation Factor eIF4E similarity (8) #227 - Nov 2018 Telomerase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (5) #143 - Nov 2011 Toll-like Receptors similarity (5) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #122 - Feb 2010 Enhanceosome similarity (7) #88 - Apr 2007 Clathrin similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (6) #150 - Jun 2012 Sliding Clamps similarity (5) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #43 - Jul 2003 Src Tyrosine Kinase similarity (3) #56 - Aug 2004 Caspases similarity (3) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #86 - Feb 2007 Exosomes similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

S2: 18S ribosomal RNA

SA: 40S ribosomal protein SA

SB: 40S ribosomal protein S3a

SD: 40S ribosomal protein S3

SE: 40S ribosomal protein S4, X isoform

SF: 40S ribosomal protein S5

SH: 40S ribosomal protein S7

SI: 40S ribosomal protein S8

SK: 40S ribosomal protein S10

SL: 40S ribosomal protein S11

SP: 40S ribosomal protein S15

SQ: 40S ribosomal protein S16

SR: 40S ribosomal protein S17

SS: 40S ribosomal protein S18

ST: 40S ribosomal protein S19

SU: 40S ribosomal protein S20

SV: 40S ribosomal protein S21

SX: 40S ribosomal protein S23

Sa: 40S ribosomal protein S26

Sc: 40S ribosomal protein S28

Sd: 40S ribosomal protein S29

Sg: Receptor of activated protein C kinase 1

SC: 40S ribosomal protein S2

SG: 40S ribosomal protein S6

SJ: 40S ribosomal protein S9

SM: 40S ribosomal protein S12

SN: 40S ribosomal protein S13

SO: 40S ribosomal protein S14

SW: 40S ribosomal protein S15a

SY: 40S ribosomal protein S24

SZ: 40S ribosomal protein S25

Sb: 40S ribosomal protein S27

Se: 40S ribosomal protein S30

Sf: 40S ribosomal protein S27a

A: 60S ribosomal protein L8

B: 60S ribosomal protein L3

C: 60S ribosomal protein L4

D: 5.8S ribosomal RNA

E: 5S ribosomal RNA

F: 60S ribosomal protein L5

G: 60S ribosomal protein L6

H: 60S ribosomal protein L7

I: 60S ribosomal protein L7a

J: 60S ribosomal protein L9

K: 60S ribosomal protein L10

L: 60S ribosomal protein L11

M: 60S ribosomal protein L13

N: 60S ribosomal protein L14

O: 60S ribosomal protein L15

P: 60S ribosomal protein L13a

Q: 60S ribosomal protein L17

R: 60S ribosomal protein L18

S: 60S ribosomal protein L19

T: 60S ribosomal protein L18a

U: 60S ribosomal protein L21

V: 60S ribosomal protein L22

W: 60S ribosomal protein L23

X: 60S ribosomal protein L24

Y: 60S ribosomal protein L23a

Z: 60S ribosomal protein L26

a: 60S ribosomal protein L27

b: 60S ribosomal protein L27a

c: 60S ribosomal protein L29

d: 60S ribosomal protein L30

e: 60S ribosomal protein L31

f: 60S ribosomal protein L32

g: 60S ribosomal protein L35a

h: 60S ribosomal protein L34

i: 60S ribosomal protein L35

j: 60S ribosomal protein L36

k: 60S ribosomal protein L37

l: 60S ribosomal protein L38

m: 60S ribosomal protein L39

n: 60S ribosomal protein L40

o: 60S ribosomal protein L41

p: 60S ribosomal protein L36a

q: 60S ribosomal protein L37a

r: 60S ribosomal protein L28

t: 28S ribosomal RNA

u: tRNA

v: tRNA

w: mRNA

y: Nascent chain

hetero molecules

3.18 MDa, 83 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: microscopy

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RNA chain , 7 types, 7 molecules S2DEtuvw

#1: RNA chain	18S ribosomal RNA Mass: 553505.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#38: RNA chain	5.8S ribosomal RNA Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#39: RNA chain	5S ribosomal RNA Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#79: RNA chain	28S ribosomal RNA Mass: 1168718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#80: RNA chain	tRNA Mass: 24414.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#81: RNA chain	tRNA Mass: 24436.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#82: RNA chain	mRNA Mass: 3193.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSeSf

#2: Protein	40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2 Mass: 24774.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#3: Protein	40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1 Mass: 24888.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#4: Protein	40S ribosomal protein S3 / Small ribosomal subunit protein uS3 Mass: 25041.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23396
#5: Protein	40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4 Mass: 29292.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#6: Protein	40S ribosomal protein S5 / Small ribosomal subunit protein uS7 Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#7: Protein	40S ribosomal protein S7 / Small ribosomal subunit protein eS7 Mass: 21603.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#8: Protein	40S ribosomal protein S8 / Small ribosomal subunit protein eS8 Mass: 23816.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#9: Protein	40S ribosomal protein S10 / Small ribosomal subunit protein eS10 Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#10: Protein	40S ribosomal protein S11 / Small ribosomal subunit protein uS17 Mass: 17785.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#11: Protein	40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19 Mass: 14931.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#12: Protein	40S ribosomal protein S16 / Small ribosomal subunit protein uS9 Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#13: Protein	40S ribosomal protein S17 / Small ribosomal subunit protein eS17 Mass: 15446.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#14: Protein	40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13 Mass: 17029.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#15: Protein	40S ribosomal protein S19 / Small ribosomal subunit protein eS19 Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#16: Protein	40S ribosomal protein S20 / Small ribosomal subunit protein uS10 Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#17: Protein	40S ribosomal protein S21 / Small ribosomal subunit protein eS21 Mass: 8977.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#18: Protein	40S ribosomal protein S23 / Small ribosomal subunit protein uS12 Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#19: Protein	40S ribosomal protein S26 / Small ribosomal subunit protein eS26 Mass: 11742.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#20: Protein	40S ribosomal protein S28 / Small ribosomal subunit protein eS28 Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#21: Protein	40S ribosomal protein S29 / Small ribosomal subunit protein uS14 Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#23: Protein	40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5 Mass: 24330.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#24: Protein	40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6 Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#25: Protein	40S ribosomal protein S9 / Small ribosomal subunit protein uS4 Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#26: Protein	40S ribosomal protein S12 / Small ribosomal subunit protein eS12 Mass: 13217.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#27: Protein	40S ribosomal protein S13 / Small ribosomal subunit protein uS15 Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#28: Protein	40S ribosomal protein S14 / Small ribosomal subunit protein uS11 Mass: 14657.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#29: Protein	40S ribosomal protein S15a / Small ribosomal subunit protein uS8 Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#30: Protein	40S ribosomal protein S24 / Small ribosomal subunit protein eS24 Mass: 15203.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#31: Protein	40S ribosomal protein S25 / Small ribosomal subunit protein eS25 Mass: 8253.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#32: Protein	40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27 Mass: 9210.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#33: Protein	40S ribosomal protein S30 Mass: 6452.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: E9PR30, UniProt: P62861*PLUS
#34: Protein	40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80 Mass: 7884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

+
60S ribosomal protein ... , 42 types, 42 molecules ABCFGHIJKLMNOPQRSTUVWXYZabcdef...

#35: Protein	60S ribosomal protein L8 / Large ribosomal subunit protein uL2 Mass: 27456.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#36: Protein	60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3 Mass: 45564.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#37: Protein	60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4 Mass: 41171.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#40: Protein	60S ribosomal protein L5 / Large ribosomal subunit protein uL18 Mass: 34091.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#41: Protein	60S ribosomal protein L6 / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107 Mass: 28378.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#42: Protein	60S ribosomal protein L7 / Large ribosomal subunit protein uL30 Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#43: Protein	60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3 Mass: 26724.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#44: Protein	60S ribosomal protein L9 / Large ribosomal subunit protein uL6 Mass: 21770.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#45: Protein	60S ribosomal protein L10 / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM Mass: 24381.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#46: Protein	60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5 Mass: 19270.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#47: Protein	60S ribosomal protein L13 / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13 Mass: 23574.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#48: Protein	60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14 Mass: 16220.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#49: Protein	60S ribosomal protein L15 / Large ribosomal subunit protein eL15 Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#50: Protein	60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13 Mass: 22820.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#51: Protein	60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1 Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#52: Protein	60S ribosomal protein L18 / Large ribosomal subunit protein eL18 Mass: 21556.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#53: Protein	60S ribosomal protein L19 / Large ribosomal subunit protein eL19 Mass: 21742.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#54: Protein	60S ribosomal protein L18a / Large ribosomal subunit protein eL20 Mass: 20661.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#55: Protein	60S ribosomal protein L21 / Large ribosomal subunit protein eL21 Mass: 18276.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#56: Protein	60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22 Mass: 11481.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#57: Protein	60S ribosomal protein L23 Mass: 13828.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTQ7, UniProt: P62829*PLUS
#58: Protein	60S ribosomal protein L24 / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24 Mass: 7253.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#59: Protein	60S ribosomal protein L23a / Large ribosomal subunit protein uL23 Mass: 13614.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#60: Protein	60S ribosomal protein L26 / Large ribosomal subunit protein uL24 Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#61: Protein	60S ribosomal protein L27 / Large ribosomal subunit protein eL27 Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#62: Protein	60S ribosomal protein L27a / Large ribosomal subunit protein uL15 Mass: 16473.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#63: Protein	60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29 Mass: 13965.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#64: Protein	60S ribosomal protein L30 / Large ribosomal subunit protein eL30 Mass: 11500.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#65: Protein	60S ribosomal protein L31 / Large ribosomal subunit protein eL31 Mass: 12506.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#66: Protein	60S ribosomal protein L32 / Large ribosomal subunit protein eL32 Mass: 15179.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#67: Protein	60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33 Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#68: Protein	60S ribosomal protein L34 / Large ribosomal subunit protein eL34 Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#69: Protein	60S ribosomal protein L35 / Large ribosomal subunit protein uL29 Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#70: Protein	60S ribosomal protein L36 / Large ribosomal subunit protein eL36 Mass: 11373.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#71: Protein	60S ribosomal protein L37 / G1.16 / Large ribosomal subunit protein eL37 Mass: 9864.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#72: Protein	60S ribosomal protein L38 / Large ribosomal subunit protein eL38 Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#73: Protein/peptide	60S ribosomal protein L39 / Large ribosomal subunit protein eL39 Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#74: Protein/peptide	60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 Mass: 5957.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#75: Protein/peptide	60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41 Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#76: Protein	60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42 Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#77: Protein	60S ribosomal protein L37a / Large ribosomal subunit protein eL43 Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#78: Protein	60S ribosomal protein L28 / Large ribosomal subunit protein eL28 Mass: 13991.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779

-
Protein / Protein/peptide , 2 types, 2 molecules Sgy

#22: Protein	Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1 Mass: 34568.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#83: Protein/peptide	Nascent chain Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

#22: Protein

Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...

Mass: 34568.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human) / References: UniProt: P63244

#83: Protein/peptide

Nascent chain

Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human)

-
Non-polymers , 4 types, 52 molecules

#84: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg
#85: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#86: Chemical	ChemComp-MVM / N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide Mass: 433.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₂₀ClN₇O
#87: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component	Name: Structure of human ribosome nascent chain complex stalled by a drug-like molecule (USO1_RNC) Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Details: unspecified
Vitrification	Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD
Image recording	Electron dose: 55 e/Å² / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correction	Type: NONE
3D reconstruction	Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38314 / Symmetry type: POINT

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RNA chain , 7 types, 7 molecules S2DEtuvw

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40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSeSf

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60S ribosomal protein ... , 42 types, 42 molecules ABCFGHIJKLMNOPQRSTUVWXYZabcdef...

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-RNA chain , 7 types, 7 molecules S2DEtuvw

+40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSeSf

+60S ribosomal protein ... , 42 types, 42 molecules ABCFGHIJKLMNOPQRSTUVWXYZabcdef...

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RNA chain , 7 types, 7 molecules S2DEtuvw

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40S ribosomal protein ... , 32 types, 32 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSeSf

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60S ribosomal protein ... , 42 types, 42 molecules ABCFGHIJKLMNOPQRSTUVWXYZabcdef...

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Protein / Protein/peptide , 2 types, 2 molecules Sgy

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