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- PDB-4v6x: Structure of the human 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 4v6x
TitleStructure of the human 80S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • (60S acidic ribosomal protein ...) x 3
  • (60S ribosomal protein ...) x 44
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • E-tRNA
  • Elongation factor 2EEF2
  • Guanine nucleotide-binding protein subunit beta-2-like 1
  • Plasminogen activator inhibitor 1 RNA-binding protein
KeywordsRIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry
Function / homology
Function and homology information


Synthesis of diphthamide-EEF2 / cytoplasmic translational elongation / ribosome hibernation / PML body organization / translation elongation factor binding / SUMO binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist ...Synthesis of diphthamide-EEF2 / cytoplasmic translational elongation / ribosome hibernation / PML body organization / translation elongation factor binding / SUMO binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 80S initiation complex / protein tyrosine kinase inhibitor activity / negative regulation of protein neddylation / translation at presynapse / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / IRE1-RACK1-PP2A complex / nucleolus organization / ribosomal protein import into nucleus / 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 / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / exit from mitosis / protein-DNA complex disassembly / TNFR1-mediated ceramide production / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of DNA repair / negative regulation of RNA splicing / laminin receptor activity / optic nerve development / TORC2 complex binding / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / GAIT complex / G1 to G0 transition / neural crest cell differentiation / retinal ganglion cell axon guidance / NF-kappaB complex / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / middle ear morphogenesis / aggresome / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / translational elongation / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / response to aldosterone / negative regulation of Wnt signaling pathway / homeostatic process / Uptake and function of diphtheria toxin / positive regulation of T cell receptor signaling pathway / lung morphogenesis / macrophage chemotaxis / protein kinase activator activity / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / Protein hydroxylation / male meiosis I / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency
Similarity search - Function
Ribosomal protein P2 / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Ubiquitin-like protein FUBI ...Ribosomal protein P2 / Intracellular hyaluronan-binding protein 4, N-terminal domain / Intracellular hyaluronan-binding protein 4 N-terminal / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Ubiquitin-like protein FUBI / 40S ribosomal protein SA / 60s Acidic ribosomal protein / 40S ribosomal protein SA, C-terminal domain / 60S acidic ribosomal protein P0 / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / : / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / EF-G domain III/V-like / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein S19e, conserved site / : / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Tr-type G domain, conserved site / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein S21e
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein P1 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein P1 / Large ribosomal subunit protein P2 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Elongation factor 2 / 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 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 / SERPINE1 mRNA-binding protein 1 / Ribosomal protein uL16-like / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsAnger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R.
CitationJournal: Nature / Year: 2013
Title: Structures of the human and Drosophila 80S ribosome.
Authors: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann /
Abstract: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J3A, 3J3D, 3J3B, 3J3F
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 8, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.5Feb 1, 2023Group: Database references
Category: citation_author / database_2 / pdbx_database_related
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

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Structure visualization

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Assembly

Deposited unit
Az: Elongation factor 2
Ag: Guanine nucleotide-binding protein subunit beta-2-like 1
AU: 40S ribosomal protein S20
AK: 40S ribosomal protein S10
AO: 40S ribosomal protein S14
AX: 40S ribosomal protein S23
AM: 40S ribosomal protein S12
AS: 40S ribosomal protein S18
Ad: 40S ribosomal protein S29
AN: 40S ribosomal protein S13
AL: 40S ribosomal protein S11
AR: 40S ribosomal protein S17
AP: 40S ribosomal protein S15
AT: 40S ribosomal protein S19
AB: 40S ribosomal protein S3a
AA: 40S ribosomal protein SA
AV: 40S ribosomal protein S21
AY: 40S ribosomal protein S24
AZ: 40S ribosomal protein S25
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
Ac: 40S ribosomal protein S28
AD: 40S ribosomal protein S3
Ae: 40S ribosomal protein S30
Af: 40S ribosomal protein S27a
AJ: 40S ribosomal protein S9
AE: 40S ribosomal protein S4, X isoform
AC: 40S ribosomal protein S2
AG: 40S ribosomal protein S6
AF: 40S ribosomal protein S5
AH: 40S ribosomal protein S7
AW: 40S ribosomal protein S15a
AI: 40S ribosomal protein S8
AQ: 40S ribosomal protein S16
Ah: Plasminogen activator inhibitor 1 RNA-binding protein
B2: 18S ribosomal RNA
BC: E-tRNA
Cz: 60S ribosomal protein L10a
Cq: 60S acidic ribosomal protein P0
CK: 60S ribosomal protein L12
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: 60S ribosomal protein L23
CM: 60S ribosomal protein L14
Ca: 60S ribosomal protein L27a
CN: 60S ribosomal protein L15
CI: 60S ribosomal protein L10-like
CD: 60S ribosomal protein L5
CQ: 60S ribosomal protein L18
CR: 60S ribosomal protein L19
CA: 60S ribosomal protein L8
CS: 60S ribosomal protein L18a
CT: 60S ribosomal protein L21
CP: 60S ribosomal protein L17
CU: 60S ribosomal protein L22
CX: 60S ribosomal protein L23a
CY: 60S ribosomal protein L26
CW: 60S ribosomal protein L24
CZ: 60S ribosomal protein L27
Cr: 60S ribosomal protein L28
Ch: 60S ribosomal protein L35
Cb: 60S ribosomal protein L29
CB: 60S ribosomal protein L3
CF: 60S ribosomal protein L7
Cc: 60S ribosomal protein L30
Cd: 60S ribosomal protein L31
Ce: 60S ribosomal protein L32
Cf: 60S ribosomal protein L35a
Cg: 60S ribosomal protein L34
Ci: 60S ribosomal protein L36
Cj: 60S ribosomal protein L37
Ck: 60S ribosomal protein L38
Cl: 60S ribosomal protein L39
CC: 60S ribosomal protein L4
Cm: 60S ribosomal protein L40
Cn: 60S ribosomal protein L41
Cp: 60S ribosomal protein L37a
Co: 60S ribosomal protein L36a
CJ: 60S ribosomal protein L11
CH: 60S ribosomal protein L9
CE: 60S ribosomal protein L6
CG: 60S ribosomal protein L7a
Cs: 60S acidic ribosomal protein P1
Ct: 60S acidic ribosomal protein P1
Cu: 60S acidic ribosomal protein P2
Cv: 60S acidic ribosomal protein P2
A5: 28S ribosomal RNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)4,051,27589
Polymers4,051,27589
Non-polymers00
Water0
1


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

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Components

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Protein , 3 types, 3 molecules AzAgAh

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 95463.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13639
#2: 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
#35: Protein Plasminogen activator inhibitor 1 RNA-binding protein / PAI1 RNA-binding protein 1 / PAI-RBP1 / SERPINE1 mRNA-binding protein 1


Mass: 45051.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NC51

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

#3: 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
#4: 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
#5: 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
#6: 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
#7: Protein 40S ribosomal protein S12 /


Mass: 14548.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#8: 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
#9: 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
#10: 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
#11: 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
#12: Protein 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: Protein 40S ribosomal protein S27a /


Mass: 9445.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#26: 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
#27: Protein 40S ribosomal protein S4, X isoform / Ribosome / 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
#28: 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
#29: 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
#30: Protein 40S ribosomal protein S5 / / 40S ribosomal protein S5 / N-terminally processed


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#31: 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
#32: 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
#33: 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
#34: 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

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RNA chain , 5 types, 5 molecules B2BCA5A7A8

#36: RNA chain 18S ribosomal RNA /


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: X03205
#37: RNA chain E-tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: K00328
#85: RNA chain 28S ribosomal RNA /


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_003287
#86: RNA chain 5S ribosomal RNA /


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: V00589
#87: RNA chain 5.8S ribosomal RNA /


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_046235

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60S ribosomal protein ... , 44 types, 44 molecules CzCKCOCLCVCMCaCNCICDCQCRCACSCTCPCUCXCYCWCZCrChCbCBCFCcCdCeCf...

#38: 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
#40: Protein 60S ribosomal protein L12 /


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: Protein 60S ribosomal protein L40 / / CEP52


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#76: 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
#77: 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
#78: 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
#79: 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
#80: 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
#81: 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
#82: 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

-
60S acidic ribosomal protein ... , 3 types, 5 molecules CqCsCtCuCv

#39: Protein 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
#83: Protein 60S acidic ribosomal protein P1


Mass: 11521.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05386
#84: Protein 60S acidic ribosomal protein P2 / Renal carcinoma antigen NY-REN-44


Mass: 11676.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05387

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S human ribosome from PBMCs / Type: RIBOSOME
Molecular weightValue: 4.5 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 90000 X / Calibrated magnification: 90000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: each subvolume
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection matching / Resolution: 5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 343343 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms46276 0 0 0 46276

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