PDB-9c3h: Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in ...

ID or keywords:

Entry

Database: PDB / ID: 9c3h

Title

Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.

Components

(Large ribosomal subunit protein ...) x 41
(Small ribosomal subunit protein ...) x 30
18S rRNA
28S rRNA
5.8S rRNA
5S rRNA
CCR4-NOT transcription complex subunit 3
FAU ubiquitin-like and ribosomal protein S30
Isoform 3 of Small ribosomal subunit protein eS24
Nascent chain
Receptor of activated protein C kinase 1
Ubiquitin-40S ribosomal protein S27a
mRNA
tRNA-ARG,CCG-1

Keywords

RIBOSOME / mRNA degradation / CCR4-NOT complex / tRNA

Function / homology

Function and homology information

CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex ...CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / optic nerve development / regulation of translation involved in cellular response to UV / M-decay: degradation of maternal mRNAs by maternally stored factors / 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 / negative regulation of formation of translation preinitiation complex / positive regulation of respiratory burst involved in inflammatory response / regulation of G1 to G0 transition / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / protein-DNA complex disassembly / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulatory ncRNA-mediated gene silencing / 90S preribosome assembly / retinal ganglion cell axon guidance / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / supercoiled DNA binding / TORC2 complex binding / neural crest cell differentiation / alpha-beta T cell differentiation / G1 to G0 transition / NF-kappaB complex / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / middle ear morphogenesis / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / homeostatic process / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / lung morphogenesis / monocyte chemotaxis / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / positive regulation of GTPase activity / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / blastocyst development / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function

CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5 C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5 C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / 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 L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / 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 S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / S27a-like superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1.
Similarity search - Domain/homology

: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / CCR4-NOT transcription complex subunit 3 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / CCR4-NOT transcription complex subunit 3 / 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 eL36
Similarity search - Component

Biological species

Homo sapiens (human)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å

Authors

Erzberger, J.P. / Cruz, V.E.

Funding support

United States, 7items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01CA282036	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	RR150074	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RP220309	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RP170644	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RR150074	United States
Welch Foundation	I-1961	United States
Welch Foundation	I-1897	United States

Citation

Journal: Science / Year: 2024
Title: Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.
Authors: Xiaoqiang Zhu / Victor Emmanuel Cruz / He Zhang / Jan P Erzberger / Joshua T Mendell /

Abstract: The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. ...

History

Deposition	Jun 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9c3h.cif.gz	5.6 MB	Display	PDBx/mmCIF format
PDB format	pdb9c3h.ent.gz		Display	PDB format
PDBx/mmJSON format	9c3h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9c3h_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9c3h_full_validation.pdf.gz	2.3 MB	Display
Data in XML	9c3h_validation.xml.gz	360.2 KB	Display
Data in CIF	9c3h_validation.cif.gz	657.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c3/9c3h ftp://data.pdbj.org/pub/pdb/validation_reports/c3/9c3h	HTTPS FTP

-
Related structure data

Related structure data	45170MC 9c3iC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (83) #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 (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 (235) #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 (114) #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 (80) #230 - Feb 2019 Initiation Factor eIF4E similarity (9) #106 - Oct 2008 Poly(A) Polymerase similarity (6) #227 - Nov 2018 Telomerase similarity (2) #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 (8) #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) #86 - Feb 2007 Exosomes similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #213 - Sep 2017 Sirtuins similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (3) #56 - Aug 2004 Caspases similarity (3) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex 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

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (83)
#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 (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 (235)
#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 (114)
#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 (80)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (9)
#106 - Oct 2008
Poly(A) Polymerase
similarity (6)
#227 - Nov 2018
Telomerase
similarity (2)
#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 (8)
#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)
#86 - Feb 2007
Exosomes
similarity (2)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (8)
#68 - Aug 2005
Neurotrophins
similarity (3)
#213 - Sep 2017
Sirtuins
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (3)
#56 - Aug 2004
Caspases
similarity (3)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#165 - Sep 2013
Designed Protein Cages
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
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)

Deposited unit

L1: 5.8S rRNA

L5: 28S rRNA

L8: Large ribosomal subunit protein uL18

L9: 5S rRNA

LB: Large ribosomal subunit protein uL3

S4: tRNA-ARG,CCG-1

LC: Large ribosomal subunit protein uL4

LD: Large ribosomal subunit protein uL2

LE: Large ribosomal subunit protein uL24

LF: Large ribosomal subunit protein uL30

LG: Large ribosomal subunit protein eL8

LH: Large ribosomal subunit protein uL6

LI: Large ribosomal subunit protein eL32

LJ: Large ribosomal subunit protein uL5

LK: Large ribosomal subunit protein eL6

LM: Large ribosomal subunit protein eL14

LN: Large ribosomal subunit protein eL15

LO: Large ribosomal subunit protein uL29

LP: Large ribosomal subunit protein eL37

LQ: Large ribosomal subunit protein eL13

LR: Large ribosomal subunit protein eL19

LS: Large ribosomal subunit protein eL20

LT: Large ribosomal subunit protein eL21

LU: Large ribosomal subunit protein eL39

LV: Large ribosomal subunit protein uL14

LW: Large ribosomal subunit protein eL24

LY: Large ribosomal subunit protein uL13

LZ: Large ribosomal subunit protein eL27

La: Large ribosomal subunit protein uL15

Lb: Large ribosomal subunit protein eL29

Lc: Large ribosomal subunit protein eL30

Ld: Large ribosomal subunit protein eL31

Le: Large ribosomal subunit protein eL42

Lf: Large ribosomal subunit protein eL33

Lg: Large ribosomal subunit protein eL34

Lh: Large ribosomal subunit protein uL22

Li: Large ribosomal subunit protein eL36

Lj: Large ribosomal subunit protein eL18

Lk: Large ribosomal subunit protein eL38

Ll: Large ribosomal subunit protein eL28

Lm: Large ribosomal subunit protein eL22

Ln: Large ribosomal subunit protein uL23

Lo: Large ribosomal subunit protein eL40

Lp: Large ribosomal subunit protein eL43

Lz: Large ribosomal subunit protein uL16

NC: Nascent chain

S1: Small ribosomal subunit protein eS1

S2: 18S rRNA

S5: mRNA

SA: Small ribosomal subunit protein uS2

SB: CCR4-NOT transcription complex subunit 3

SC: Small ribosomal subunit protein uS5

SD: Small ribosomal subunit protein uS7

SE: Small ribosomal subunit protein eS4, X isoform

SG: Small ribosomal subunit protein eS6

SH: Small ribosomal subunit protein eS7

SI: Small ribosomal subunit protein eS8

SJ: Small ribosomal subunit protein uS4

SK: Small ribosomal subunit protein uS3

SL: Small ribosomal subunit protein uS17

SM: Small ribosomal subunit protein eS10

SN: Small ribosomal subunit protein uS15

SO: Small ribosomal subunit protein uS11

SP: Small ribosomal subunit protein uS19

SQ: Small ribosomal subunit protein uS9

SS: Small ribosomal subunit protein eS17

ST: Small ribosomal subunit protein uS13

SU: Small ribosomal subunit protein eS19

SV: Small ribosomal subunit protein eS21

SW: Small ribosomal subunit protein uS8

SX: Small ribosomal subunit protein uS12

SY: Isoform 3 of Small ribosomal subunit protein eS24

SZ: Small ribosomal subunit protein uS10

Sa: Small ribosomal subunit protein eS26

Sb: Small ribosomal subunit protein eS27

Sc: Small ribosomal subunit protein eS25

Sd: Small ribosomal subunit protein eS28

Se: FAU ubiquitin-like and ribosomal protein S30

Sf: Small ribosomal subunit protein uS14

Sg: Receptor of activated protein C kinase 1

So: Small ribosomal subunit protein eS32

Sy: Small ribosomal subunit protein eS12

Sz: Ubiquitin-40S ribosomal protein S27a

hetero molecules

3.89 MDa, 83 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

-
RNA chain , 6 types, 6 molecules L1L5L9S4S2S5

#1: RNA chain	5.8S rRNA Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#2: RNA chain	28S rRNA Mass: 1640938.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: 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
#6: RNA chain	tRNA-ARG,CCG-1 Mass: 24661.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#48: RNA chain	18S rRNA Mass: 603582.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#49: RNA chain	mRNA Mass: 2847.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

#3: Protein	Large ribosomal subunit protein uL18 / 60S ribosomal protein L5 Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#5: Protein	Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#7: Protein	Large ribosomal subunit protein uL4 / 60S ribosomal protein L4 / 60S ribosomal protein L1 Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#8: Protein	Large ribosomal subunit protein uL2 / 60S ribosomal protein L8 Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#9: Protein	Large ribosomal subunit protein uL24 / 60S ribosomal protein L26 Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#10: Protein	Large ribosomal subunit protein uL30 / 60S ribosomal protein L7 Mass: 29306.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#11: Protein	Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a / PLA-X polypeptide / Surfeit locus protein 3 Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#12: Protein	Large ribosomal subunit protein uL6 / 60S ribosomal protein L9 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	Large ribosomal subunit protein eL32 / 60S ribosomal protein L32 Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#14: Protein	Large ribosomal subunit protein uL5 / 60S ribosomal protein L11 / CLL-associated antigen KW-12 Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#15: Protein	Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107 Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#16: Protein	Large ribosomal subunit protein eL14 / 60S ribosomal protein L14 / CAG-ISL 7 Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#17: Protein	Large ribosomal subunit protein eL15 / 60S ribosomal protein L15 Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#18: Protein	Large ribosomal subunit protein uL29 / 60S ribosomal protein L35 Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#19: Protein	Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16 Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#20: Protein	Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1 Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#21: Protein	Large ribosomal subunit protein eL19 / 60S ribosomal protein L19 Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#22: Protein	Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#23: Protein	Large ribosomal subunit protein eL21 / 60S ribosomal protein L21 Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#24: Protein	Large ribosomal subunit protein eL39 / 60S ribosomal protein L39 Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#25: Protein	Large ribosomal subunit protein uL14 / 60S ribosomal protein L23 / 60S ribosomal protein L17 Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#26: Protein	Large ribosomal subunit protein eL24 / 60S ribosomal protein L24 / 60S ribosomal protein L30 Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#27: Protein	Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a / 23 kDa highly basic protein Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#28: Protein	Large ribosomal subunit protein eL27 / 60S ribosomal protein L27 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	Large ribosomal subunit protein uL15 / 60S ribosomal protein L27a Mass: 16619.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#30: Protein	Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP Mass: 17817.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#31: Protein	Large ribosomal subunit protein eL30 / 60S ribosomal protein L30 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	Large ribosomal subunit protein eL31 / 60S ribosomal protein L31 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	Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / ...60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#34: Protein	Large ribosomal subunit protein eL33 / 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein 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	Large ribosomal subunit protein eL34 / 60S ribosomal protein L34 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	Large ribosomal subunit protein uL22 / 60S ribosomal protein L17 / 60S ribosomal protein L23 / PD-1 Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#37: Protein	Large ribosomal subunit protein eL36 / 60S ribosomal protein L36 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	Large ribosomal subunit protein eL18 / 60S ribosomal protein L18 Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#39: Protein	Large ribosomal subunit protein eL38 / 60S ribosomal protein L38 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	Large ribosomal subunit protein eL28 / 60S ribosomal protein L28 Mass: 15679.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#41: Protein	Large ribosomal subunit protein eL22 / 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated ...60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#42: Protein	Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#43: Protein	Large ribosomal subunit protein eL40 / 60S ribosomal protein L40 Mass: 11512.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#44: Protein	Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a 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	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

-
Protein/peptide , 1 types, 1 molecules NC

#46: Protein/peptide	Nascent chain Mass: 3258.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

#47: Protein	Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / 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
#50: Protein	Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 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 Mass: 32778.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#52: Protein	Small ribosomal subunit protein uS5 / 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#53: Protein	Small ribosomal subunit protein uS7 / 40S ribosomal protein S5 Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#54: Protein	Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#55: Protein	Small ribosomal subunit protein eS6 / 40S ribosomal protein S6 / Phosphoprotein NP33 Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#56: Protein	Small ribosomal subunit protein eS7 / 40S ribosomal protein S7 Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#57: Protein	Small ribosomal subunit protein eS8 / 40S ribosomal protein S8 Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#58: Protein	Small ribosomal subunit protein uS4 / 40S ribosomal protein S9 Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#59: Protein	Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 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
#60: Protein	Small ribosomal subunit protein uS17 / 40S ribosomal protein S11 Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#61: Protein	Small ribosomal subunit protein eS10 / 40S ribosomal protein S10 Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#62: Protein	Small ribosomal subunit protein uS15 / 40S ribosomal protein S13 Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#63: Protein	Small ribosomal subunit protein uS11 / 40S ribosomal protein S14 Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#64: Protein	Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#65: Protein	Small ribosomal subunit protein uS9 / 40S ribosomal protein S16 Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#66: Protein	Small ribosomal subunit protein eS17 / 40S ribosomal protein S17 Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#67: Protein	Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3 Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#68: Protein	Small ribosomal subunit protein eS19 / 40S ribosomal protein S19 Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#69: Protein	Small ribosomal subunit protein eS21 / 40S ribosomal protein S21 Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#70: Protein	Small ribosomal subunit protein uS8 / 40S ribosomal protein S15a Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#71: Protein	Small ribosomal subunit protein uS12 / 40S ribosomal protein S23 Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#73: Protein	Small ribosomal subunit protein uS10 / 40S ribosomal protein S20 Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#74: Protein	Small ribosomal subunit protein eS26 / 40S ribosomal protein S26 Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#75: Protein	Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#76: Protein	Small ribosomal subunit protein eS25 / 40S ribosomal protein S25 Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#77: Protein	Small ribosomal subunit protein eS28 / 40S ribosomal protein S28 Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#79: Protein	Small ribosomal subunit protein uS14 / 40S ribosomal protein S29 Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#81: Protein/peptide	Small ribosomal subunit protein eS32 / 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
#82: Protein	Small ribosomal subunit protein eS12 / 40S ribosomal protein S12 Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398

-
Protein , 5 types, 5 molecules SBSYSeSgSz

#51: Protein	CCR4-NOT transcription complex subunit 3 / CCR4-associated factor 3 / Leukocyte receptor cluster member 2 Mass: 64125.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75175
#72: Protein	Isoform 3 of Small ribosomal subunit protein eS24 / 40S ribosomal protein S24 Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#78: Protein	FAU ubiquitin-like and ribosomal protein S30 Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#80: 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
#83: 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

-
Non-polymers , 5 types, 9914 molecules

#84: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: Mg
#85: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: K
#86: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#87: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#88: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9485 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Component	Name: 80S ribosome in complex with CNOT3 and P-site tRNA ARG CCG-1 Type: RIBOSOME / Entity ID: #1-#54, #56-#83 / Source: NATURAL
Molecular weight	Value: 4.3 MDa / Experimental value: NO
Source (natural)	Organism: Homo sapiens (human)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 / Nominal defocus max: 1900 nm / Nominal defocus min: 600 nm
Image recording	Electron dose: 17 e/Å² / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correction	Type: NONE
3D reconstruction	Resolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276000 / Symmetry type: POINT

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
RNA chain , 6 types, 6 molecules L1L5L9S4S2S5

+
Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

-
Protein/peptide , 1 types, 1 molecules NC

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

-
Protein , 5 types, 5 molecules SBSYSeSgSz

-
Non-polymers , 5 types, 9914 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Electron microscopy imaging

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-RNA chain , 6 types, 6 molecules L1L5L9S4S2S5

+Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

-Protein/peptide , 1 types, 1 molecules NC

+Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

-Protein , 5 types, 5 molecules SBSYSeSgSz

-Non-polymers , 5 types, 9914 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Electron microscopy imaging

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
RNA chain , 6 types, 6 molecules L1L5L9S4S2S5

+
Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...

-
Protein/peptide , 1 types, 1 molecules NC

+
Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy

-
Protein , 5 types, 5 molecules SBSYSeSgSz

-
Non-polymers , 5 types, 9914 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Electron microscopy imaging

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi