PDB-8yop: Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

ID or keywords:

Entry

Database: PDB / ID: 8yop

Title

Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

Components

(40S ribosomal protein ...) x 31
(60S ribosomal protein ...) x 42
(Large ribosomal subunit protein ...) x 2
18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
Receptor of activated protein C kinase 1
Ubiquitin-40S ribosomal protein S27a
Ubiquitin-60S ribosomal protein L40

Keywords

RIBOSOME / Tigecycline / antibiotic

Function / homology

Function and homology information

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

60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 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 ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 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 / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / : / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1.
Similarity search - Domain/homology

: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / 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 uL11 / 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 uL1 / 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 eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å

Authors

Li, X. / Wang, M. / Denk, T. / Cheng, J.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2024
Title: Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Authors: Xiang Li / Mengjiao Wang / Timo Denk / Robert Buschauer / Yi Li / Roland Beckmann / Jingdong Cheng /

Abstract: Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, ...

History

Deposition	Mar 13, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8yop.cif.gz	4.8 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	8yop_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8yop_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8yop_validation.xml.gz	352.3 KB	Display
Data in CIF	8yop_validation.cif.gz	621.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/8yop ftp://data.pdbj.org/pub/pdb/validation_reports/yo/8yop	HTTPS FTP

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Related structure data

Related structure data	39456MC 36836C 36837C 36838C 36839C 36945C 38629C 38630C 38631C 38632C 38633C 38634C 38635C 38636C 38637C 38638C 38639C 39455C 8k2aC 8k2bC 8k2cC 8k2dC 8k82C 8xsxC 8xsyC 8xszC 8xt0C 8xt1C 8xt2C 8xt3C 8yooC M: map data used to model this data C: citing same article (ref.)
Similar structure data	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 (98) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #10 - Oct 2000 Ribosome similarity (84) #157 - Jan 2013 Transfer-Messenger RNA similarity (12) #253 - Jan 2021 Expressome similarity (8) #260 - Aug 2021 Ribonuclease P similarity (8) #161 - May 2013 Ricin similarity (243) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #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) #266 - Feb 2022 Oligosaccharyltransferase similarity (121) #60 - Dec 2004 Ubiquitin similarity (83) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #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 (5) #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) #163 - Jul 2013 HIV Capsid similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase 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) #195 - Mar 2016 RAF Protein Kinases similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

L5: 28S rRNA

L7: 5S rRNA

L8: 5.8S rRNA

LA: 60S ribosomal protein L8

LB: 60S ribosomal protein L3

LC: 60S ribosomal protein L4

LD: 60S ribosomal protein L5

LE: 60S ribosomal protein L6

LF: 60S ribosomal protein L7

LG: 60S ribosomal protein L7a

LH: 60S ribosomal protein L9

LI: Large ribosomal subunit protein uL16

LJ: 60S ribosomal protein L11

LL: 60S ribosomal protein L13

LM: 60S ribosomal protein L14

LN: 60S ribosomal protein L15

LO: 60S ribosomal protein L13a

LP: 60S ribosomal protein L17

LQ: 60S ribosomal protein L18

LR: 60S ribosomal protein L19

LS: 60S ribosomal protein L18a

LT: 60S ribosomal protein L21

LU: 60S ribosomal protein L22

LV: 60S ribosomal protein L23

LW: 60S ribosomal protein L24

LX: 60S ribosomal protein L23a

LY: 60S ribosomal protein L26

LZ: 60S ribosomal protein L27

La: 60S ribosomal protein L27a

Lb: 60S ribosomal protein L29

Lc: 60S ribosomal protein L30

Ld: 60S ribosomal protein L31

Le: 60S ribosomal protein L32

Lf: 60S ribosomal protein L35a

Lg: 60S ribosomal protein L34

Lh: 60S ribosomal protein L35

Li: 60S ribosomal protein L36

Lj: 60S ribosomal protein L37

Lk: 60S ribosomal protein L38

Ll: 60S ribosomal protein L39

Lm: Ubiquitin-60S ribosomal protein L40

Ln: 60S ribosomal protein L41

Lo: 60S ribosomal protein L36a

Lp: 60S ribosomal protein L37a

Lr: 60S ribosomal protein L28

Ls: Large ribosomal subunit protein uL10

Lt: 60S ribosomal protein L12

Lz: 60S ribosomal protein L10a

S2: 18S rRNA

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: Ubiquitin-40S ribosomal protein S27a

hetero molecules

3.86 MDa, 82 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: electron microscopy, not applicable

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RNA chain , 4 types, 4 molecules L5L7L8S2

#1: RNA chain	28S rRNA Mass: 1640182.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 86475748
#2: RNA chain	5S rRNA Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#3: RNA chain	5.8S rRNA / Human ribosomal DNA complete repeating unit Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#49: RNA chain	18S rRNA Mass: 602752.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36162

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

#4: Protein	60S ribosomal protein L8 / Large ribosomal subunit protein uL2 Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#5: Protein	60S ribosomal protein L3 / Large ribosomal subunit protein uL3 Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#6: Protein	60S ribosomal protein L4 / Large ribosomal subunit protein uL4 Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#7: Protein	60S ribosomal protein L5 / Large ribosomal subunit protein uL18 Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#8: Protein	60S ribosomal protein L6 / Large ribosomal subunit protein eL6 Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#9: Protein	60S ribosomal protein L7 / Large ribosomal subunit protein uL30 Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#10: Protein	60S ribosomal protein L7a / Large ribosomal subunit protein eL8 Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#11: Protein	60S ribosomal protein L9 / Large ribosomal subunit protein uL6 Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#13: Protein	60S ribosomal protein L11 / Large ribosomal subunit protein uL5 Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#14: Protein	60S ribosomal protein L13 / Large ribosomal subunit protein eL13 Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#15: Protein	60S ribosomal protein L14 / Large ribosomal subunit protein eL14 Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#16: Protein	60S ribosomal protein L15 / Large ribosomal subunit protein eL15 Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#17: Protein	60S ribosomal protein L13a / Large ribosomal subunit protein uL13 Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#18: Protein	60S ribosomal protein L17 / Large ribosomal subunit protein uL22 Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#19: Protein	60S ribosomal protein L18 / Large ribosomal subunit protein eL18 Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#20: Protein	60S ribosomal protein L19 / Large ribosomal subunit protein eL19 Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#21: Protein	60S ribosomal protein L18a / Large ribosomal subunit protein eL20 Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#22: Protein	60S ribosomal protein L21 / Large ribosomal subunit protein eL21 Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#23: Protein	60S ribosomal protein L22 / Large ribosomal subunit protein eL22 Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#24: Protein	60S ribosomal protein L23 / Large ribosomal subunit protein uL14 Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#25: Protein	60S ribosomal protein L24 / Large ribosomal subunit protein eL24 Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#26: Protein	60S ribosomal protein L23a / Large ribosomal subunit protein uL23 Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#27: Protein	60S ribosomal protein L26 / Large ribosomal subunit protein uL24 Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#28: Protein	60S ribosomal protein L27 / Large ribosomal subunit protein eL27 Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#29: Protein	60S ribosomal protein L27a / Large ribosomal subunit protein uL15 Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#30: Protein	60S ribosomal protein L29 / Large ribosomal subunit protein eL29 Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#31: Protein	60S ribosomal protein L30 / Large ribosomal subunit protein eL30 Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#32: Protein	60S ribosomal protein L31 / Large ribosomal subunit protein eL31 Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#33: Protein	60S ribosomal protein L32 / Large ribosomal subunit protein eL32 Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#34: Protein	60S ribosomal protein L35a / Large ribosomal subunit protein eL33 Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#35: Protein	60S ribosomal protein L34 / Large ribosomal subunit protein eL34 Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#36: Protein	60S ribosomal protein L35 / Large ribosomal subunit protein uL29 Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#37: Protein	60S ribosomal protein L36 / Large ribosomal subunit protein eL36 Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#38: Protein	60S ribosomal protein L37 / Large ribosomal subunit protein eL37 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#39: Protein	60S ribosomal protein L38 / Large ribosomal subunit protein eL38 Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#40: Protein	60S ribosomal protein L39 / Large ribosomal subunit protein eL39 Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#42: 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
#43: Protein	60S ribosomal protein L36a / Large ribosomal subunit protein eL42 Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#44: Protein	60S ribosomal protein L37a / Large ribosomal subunit protein eL43 Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#45: Protein	60S ribosomal protein L28 / Large ribosomal subunit protein eL28 Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#47: Protein	60S ribosomal protein L12 / Large ribosomal subunit protein uL11 Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#48: Protein	60S ribosomal protein L10a / Large ribosomal subunit protein uL1 Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906

-
Large ribosomal subunit protein ... , 2 types, 2 molecules LILs

#12: Protein	Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor ...60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor suppressor QM Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#46: Protein	Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388

#12: Protein

Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Laminin receptor homolog / Protein QM / Ribosomal protein L10 / Tumor ...

Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human) / References: UniProt: P27635

#46: Protein

Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E

Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Homo sapiens (human) / References: UniProt: P05388

-
Protein , 3 types, 3 molecules LmSgSf

#41: Protein	Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1 Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#70: 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: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#82: Protein	Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80 Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

+
40S ribosomal protein ... , 31 types, 31 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSe

#50: 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: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#51: Protein	40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1 Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#52: Protein	40S ribosomal protein S3 / Small ribosomal subunit protein uS3 Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#53: Protein	40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4 Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#54: Protein	40S ribosomal protein S5 / Small ribosomal subunit protein uS7 Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#55: Protein	40S ribosomal protein S7 / Small ribosomal subunit protein eS7 Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#56: Protein	40S ribosomal protein S8 / Small ribosomal subunit protein eS8 Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#57: Protein	40S ribosomal protein S10 / Small ribosomal subunit protein eS10 Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#58: Protein	40S ribosomal protein S11 / Small ribosomal subunit protein uS17 Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#59: Protein	40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19 Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#60: 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
#61: Protein	40S ribosomal protein S17 / Small ribosomal subunit protein eS17 Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#62: Protein	40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13 Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#63: Protein	40S ribosomal protein S19 / Small ribosomal subunit protein eS19 Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#64: Protein	40S ribosomal protein S20 / Small ribosomal subunit protein uS10 Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#65: Protein	40S ribosomal protein S21 / Small ribosomal subunit protein eS21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#66: Protein	40S ribosomal protein S23 / Small ribosomal subunit protein uS12 Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#67: Protein	40S ribosomal protein S26 / Small ribosomal subunit protein eS26 Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#68: Protein	40S ribosomal protein S28 / Small ribosomal subunit protein eS28 Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#69: Protein	40S ribosomal protein S29 / Small ribosomal subunit protein uS14 Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#71: Protein	40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5 Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#72: Protein	40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6 Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#73: Protein	40S ribosomal protein S9 / Small ribosomal subunit protein uS4 Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#74: Protein	40S ribosomal protein S12 / Small ribosomal subunit protein eS12 Mass: 14548.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#75: Protein	40S ribosomal protein S13 / Small ribosomal subunit protein uS15 Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#76: Protein	40S ribosomal protein S14 / Small ribosomal subunit protein uS11 Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#77: Protein	40S ribosomal protein S15a / Small ribosomal subunit protein uS8 Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#78: Protein	40S ribosomal protein S24 / Small ribosomal subunit protein eS24 Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#79: Protein	40S ribosomal protein S25 / Small ribosomal subunit protein eS25 Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#80: Protein	40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27 Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#81: Protein	40S ribosomal protein S30 / Small ribosomal subunit protein eS30 Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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Non-polymers , 2 types, 263 molecules

#83: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 255 / Source method: obtained synthetically / Formula: Mg
#84: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Component	Name: 80S ribosome with 5um tigecycline / Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support	Grid material: COPPER / Grid type: Quantifoil R3/3
Vitrification	Cryogen name: ETHANE

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holder	Cryogen: NITROGEN
Image recording	Electron dose: 44 e/Å² / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software

ID	Name	Category
4	cryoSPARC	CTF correction
7	Coot	model fitting
9	PHENIX	model refinement
10	cryoSPARC	initial Euler assignment
11	cryoSPARC	final Euler assignment
13	cryoSPARC	3D reconstruction

CTF correction

Details: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98884 / Symmetry type: POINT

Atomic model building

Protocol: RIGID BODY FIT / Space: REAL

Atomic model building

PDB-ID: 6Z6M

6z6m

Accession code: 6Z6M / Source name: PDB / Type: experimental model

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RNA chain , 4 types, 4 molecules L5L7L8S2

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

-
Large ribosomal subunit protein ... , 2 types, 2 molecules LILs

-
Protein , 3 types, 3 molecules LmSgSf

+
40S ribosomal protein ... , 31 types, 31 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSe

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Non-polymers , 2 types, 263 molecules

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Details

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Experiment

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-RNA chain , 4 types, 4 molecules L5L7L8S2

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

-Large ribosomal subunit protein ... , 2 types, 2 molecules LILs

-Protein , 3 types, 3 molecules LmSgSf

+40S ribosomal protein ... , 31 types, 31 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSe

-Non-polymers , 2 types, 263 molecules

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-Experimental details

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RNA chain , 4 types, 4 molecules L5L7L8S2

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

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Large ribosomal subunit protein ... , 2 types, 2 molecules LILs

-
Protein , 3 types, 3 molecules LmSgSf

+
40S ribosomal protein ... , 31 types, 31 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSbSe

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Non-polymers , 2 types, 263 molecules

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Details

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Experimental details

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