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- PDB-4ug0: STRUCTURE OF THE HUMAN 80S RIBOSOME -

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Entry
Database: PDB / ID: 4ug0
TitleSTRUCTURE OF THE HUMAN 80S RIBOSOME
Components
  • (40S RIBOSOMAL PROTEIN ...) x 30
  • (60S RIBOSOMAL PROTEIN ...) x 42
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 40S RIBOSOMAL PROTEIN
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
  • HUMAN INITIATOR MET-TRNA-I
  • UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME
Function / homology
Function and homology information


positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / SRP-dependent cotranslational protein targeting to membrane / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / SRP-dependent cotranslational protein targeting to membrane / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / axial mesoderm development / negative regulation of formation of translation preinitiation complex / nucleolus organization / ribosomal protein import into nucleus / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / 90S preribosome assembly / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / laminin receptor activity / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein kinase A binding / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / optic nerve development / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / lung morphogenesis / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / male meiosis I / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / macrophage chemotaxis / SARS-CoV-1 modulates host translation machinery / viral transcription / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L1, conserved site / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L1 signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L1 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / : / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S17 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S17 / 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 / Large ribosomal subunit protein eL13 / 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 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKhatter, H. / Myasnikov, A.G. / Natchiar, S.K. / Klaholz, B.P.
CitationJournal: Nature / Year: 2015
Title: Structure of the human 80S ribosome.
Authors: Heena Khatter / Alexander G Myasnikov / S Kundhavai Natchiar / Bruno P Klaholz /
Abstract: Ribosomes are translational machineries that catalyse protein synthesis. Ribosome structures from various species are known at the atomic level, but obtaining the structure of the human ribosome has ...Ribosomes are translational machineries that catalyse protein synthesis. Ribosome structures from various species are known at the atomic level, but obtaining the structure of the human ribosome has remained a challenge; efforts to address this would be highly relevant with regard to human diseases. Here we report the near-atomic structure of the human ribosome derived from high-resolution single-particle cryo-electron microscopy and atomic model building. The structure has an average resolution of 3.6 Å, reaching 2.9 Å resolution in the most stable regions. It provides unprecedented insights into ribosomal RNA entities and amino acid side chains, notably of the transfer RNA binding sites and specific molecular interactions with the exit site tRNA. It reveals atomic details of the subunit interface, which is seen to remodel strongly upon rotational movements of the ribosomal subunits. Furthermore, the structure paves the way for analysing antibiotic side effects and diseases associated with deregulated protein synthesis.
History
DepositionMar 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Other
Revision 1.2Feb 14, 2018Group: Data collection / Structure summary / Category: em_image_scans / entity / entity_name_com / Item: _entity.pdbx_description
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
L5: 28S ribosomal RNA
L7: 5S ribosomal RNA
L8: 5.8S ribosomal RNA
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: 60S RIBOSOMAL PROTEIN L10-LIKE
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
Lz: 60S RIBOSOMAL PROTEIN L10A
S2: 18S ribosomal RNA
S6: HUMAN INITIATOR MET-TRNA-I
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-LIKE
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
Sf: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
Sg: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
SC: 40S RIBOSOMAL PROTEIN S2
SG: 40S RIBOSOMAL PROTEIN S6
SJ: 40S RIBOSOMAL PROTEIN S9
SM: 40S RIBOSOMAL PROTEIN
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,835,517326
Polymers3,829,31681
Non-polymers6,201245
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules L5L7L8S2S6

#1: RNA chain 28S ribosomal RNA / RNA (5070-MER)


Mass: 1640238.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#2: RNA chain 5S ribosomal RNA / RNA (121-MER)


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#3: RNA chain 5.8S ribosomal RNA / RNA (157-MER)


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#47: RNA chain 18S ribosomal RNA / RNA (1869-MER)


Mass: 602752.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#48: RNA chain HUMAN INITIATOR MET-TRNA-I


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: GenBank: 174924

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60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...

#4: Protein 60S RIBOSOMAL PROTEIN L8


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 / HIV-1 TAR RNA-binding protein B / TARBP-B


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 / 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
#7: Protein 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
#8: Protein 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
#9: Protein 60S RIBOSOMAL PROTEIN L7


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 / 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
#11: Protein 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
#12: Protein 60S RIBOSOMAL PROTEIN L10-LIKE


Mass: 24570.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q96L21
#13: Protein 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
#14: Protein 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
#15: Protein 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
#16: Protein 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
#17: Protein 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
#18: Protein 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
#19: Protein 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
#20: Protein 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
#21: Protein 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
#22: Protein 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
#23: Protein 60S RIBOSOMAL PROTEIN L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15


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 / 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
#25: Protein 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
#26: Protein 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
#27: Protein 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
#28: Protein 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 60S RIBOSOMAL PROTEIN L27A


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 / Cell surface heparin-binding protein HIP


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


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


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


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 / 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 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 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
#37: Protein 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 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
#39: Protein 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 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
#42: Protein/peptide 60S RIBOSOMAL PROTEIN L41 / HG12


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 / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein


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


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


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P46779
#46: Protein 60S RIBOSOMAL PROTEIN L10A / CSA-19 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P62906

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Protein , 4 types, 4 molecules LmSfSgSM

#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
#69: 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
#70: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-like ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P63244
#74: Protein 40S RIBOSOMAL PROTEIN


Mass: 14548.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)

+
40S RIBOSOMAL PROTEIN ... , 30 types, 30 molecules SASBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSNSOSWSYSZSbSe

#49: 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


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P08865
#50: Protein 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
#51: Protein 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
#52: Protein 40S RIBOSOMAL PROTEIN S4, X ISOFORM / 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
#53: Protein 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 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
#55: Protein 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
#56: Protein 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
#57: Protein 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
#58: Protein 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
#59: Protein 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
#60: Protein 40S RIBOSOMAL PROTEIN S17-LIKE


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P0CW22, UniProt: P08708*PLUS
#61: Protein 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
#62: Protein 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
#63: Protein 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
#64: Protein 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
#65: Protein 40S RIBOSOMAL PROTEIN S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P62266
#66: Protein 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
#67: Protein 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
#68: Protein 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
#71: Protein 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
#72: Protein 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
#73: Protein 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
#75: Protein 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
#76: Protein 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
#77: Protein 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
#78: Protein 40S RIBOSOMAL PROTEIN S24


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


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


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


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, 245 molecules

#82: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 239 / Source method: obtained synthetically / Formula: Mg
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN 80S RIBOSOME / Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 10, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24000 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Details: METHOD--FLEXIBLE

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