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- EMDB-44016: In situ human ribosome (Focused on 40S with SERBP1 CTD) -

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Basic information

Entry
Database: EMDB / ID: EMD-44016
TitleIn situ human ribosome (Focused on 40S with SERBP1 CTD)
Map data
Sample
  • Complex: In situ human ribosome (Focused on 40S with SERBP1 CTD)
    • Protein or peptide: x 15 types
    • RNA: x 1 types
KeywordsIn situ / RIBOSOME
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / supercoiled DNA binding / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / ion channel inhibitor activity / pigmentation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / BH3 domain binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of signal transduction by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / protein serine/threonine kinase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / TICAM1,TRAF6-dependent induction of TAK1 complex / phagocytic cup / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of translational fidelity / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / spindle assembly / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of intrinsic apoptotic signaling pathway
Similarity search - Function
: / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain ...: / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19A/S15e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S14/S29 / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / 50S ribosomal protein L30e-like / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ubiquitin family / Ubiquitin homologues / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ubiquitin domain profile. / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ubiquitin-like domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS19 ...Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsWei Z / Yong Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: In situ human ribosome (Focused on 40S with SERBP1 CTD)
Authors: Wei Z / Yong Z
History
DepositionMar 11, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44016.png

Downloads & links

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Map

FileDownload / File: emd_44016.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0146
Minimum - Maximum-0.06325879 - 0.19104815
Average (Standard dev.)0.0004825677 (±0.0048708525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44016_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44016_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : In situ human ribosome (Focused on 40S with SERBP1 CTD)

EntireName: In situ human ribosome (Focused on 40S with SERBP1 CTD)
Components
  • Complex: In situ human ribosome (Focused on 40S with SERBP1 CTD)
    • Protein or peptide: Serbp1
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: 40S ribosomal protein S5
    • Protein or peptide: 40S ribosomal protein S10
    • Protein or peptide: Small ribosomal subunit protein uS19
    • Protein or peptide: Small ribosomal subunit protein uS9
    • Protein or peptide: 40S ribosomal protein S18
    • Protein or peptide: 40S ribosomal protein S19
    • Protein or peptide: 40S ribosomal protein S20
    • Protein or peptide: 40S ribosomal protein S28
    • Protein or peptide: 40S ribosomal protein S29
    • Protein or peptide: Receptor of activated protein C kinase 1
    • Protein or peptide: Small ribosomal subunit protein eS12
    • Protein or peptide: Small ribosomal subunit protein eS25
    • Protein or peptide: Ubiquitin-40S ribosomal protein S27a
    • RNA: 18S rRNA

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Supramolecule #1: In situ human ribosome (Focused on 40S with SERBP1 CTD)

SupramoleculeName: In situ human ribosome (Focused on 40S with SERBP1 CTD)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serbp1

MacromoleculeName: Serbp1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.566574 KDa
SequenceString:
EEGPKEMTLD EWKAIQNKDR AKVEFNIRKP NEGADGQWKK GFVLHKSKEE APAANDITSQ LEINFGDLGR PYPDVDDPEA FPALA

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Macromolecule #2: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.172561 KDa
SequenceString: MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV ...String:
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAE KVATRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFIMES GAKGCEVVVS GKLRGQRAKS MKFVDGLMIH S GDPVNYYV DTAVRHVLLR QGVLGIKVKI MLPWDPTGKI GPKKPLPDHV SIVEPKDEIL PTTPISEQK

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #3: 40S ribosomal protein S5

MacromoleculeName: 40S ribosomal protein S5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.327723 KDa
SequenceString:
DIKLFGKWST DDVQINDISL QDYIAVKEKY AKYLPHSAGR YAAKRFRKAQ CPIVERLTNS MMMHGRNNGK KLMTVRIVKH AFEIIHLLT GENPLQVLVN AIINSGPRED STRIGRAGTV RRQAVDVSPL RRVNQAIWLL CTGAREAAFR NIKTIAECLA D ELINAAKG SSNSYAIKKK DELERVAKSN R

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #4: 40S ribosomal protein S10

MacromoleculeName: 40S ribosomal protein S10 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.773953 KDa
SequenceString:
MLMPKKNRIA IYELLFKEGV MVAKKDVHMP KHPELADKNV PNLHVMKAMQ SLKSRGYVKE QFAWRHFYWY LTNEGIQYLR DYLHLPPEI VPATLRRSR

UniProtKB: Small ribosomal subunit protein eS10

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Macromolecule #5: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.0926 KDa
SequenceString:
TYRGVDLDQL LDMSYEQLMQ LYSARQRRRL NRGLRRKQHS LLKRLRKAKK EAPPMEKPEV VKTHLRDMII LPEMVGSMVG VYNGKTFNQ VEIKPEMIGH YLGEFSITYK PVKHGRPGIG AT

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #6: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.249062 KDa
SequenceString:
SKGPLQSVQV FGRKKTATAV AHCKRGNGLI KVNGRPLEMI EPRTLQYKLL EPVLLLGKER FAGVDIRVRV KGGGHVAQIY AIRQSISKA LVAYYQKYVD EASKKEIKDI LIQYDRTLLV ADPRRCESKK FGGPGARARY QKSYR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #7: 40S ribosomal protein S18

MacromoleculeName: 40S ribosomal protein S18 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.029844 KDa
SequenceString:
MSLVIPEKFQ HILRVLNTNI DGRRKIAFAI TAIKGVGRRY AHVVLRKADI DLTKRAGELT EDEVERVITI MQNPRQYKIP DWFLNRQKD VKDGKYSQVL ANGLDNKLRE DLERLKKIRA HRGLRHFWGL RVRGQHTKTT GRRGRT

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #8: 40S ribosomal protein S19

MacromoleculeName: 40S ribosomal protein S19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.822219 KDa
SequenceString:
PGVTVKDVNQ QEFVRALAAF LKKSGKLKVP EWVDTVKLAK HKELAPYDEN WFYTRAASTA RHLYLRGGAG VGSMTKIYGG RQRNGVMPS HFSRGSKSVA RRVLQALEGL KMVEKDQDGG RKLTPQGQRD LDRIAGQVAA ANKK

UniProtKB: Small ribosomal subunit protein eS19

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Macromolecule #9: 40S ribosomal protein S20

MacromoleculeName: 40S ribosomal protein S20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.76589 KDa
SequenceString:
AIHRIRITLT SRNVKSLEKV CADLIRGAKE KNLKVKGPVR MPTKTLRITT RKTPCGEGSK TWDRFQMRIH KRLIDLHSPS EIVKQITSI SIEPGVEVEV TIADA

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #10: 40S ribosomal protein S28

MacromoleculeName: 40S ribosomal protein S28 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.263394 KDa
SequenceString:
RVQPIKLARV TKVLGRTGSQ GQCTQVRVEF MDDTSRSIIR NVKGPVREGD VLTLLESERE ARRL

UniProtKB: Small ribosomal subunit protein eS28

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Macromolecule #11: 40S ribosomal protein S29

MacromoleculeName: 40S ribosomal protein S29 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.559625 KDa
SequenceString:
GHQQLYWSHP RKFGQGSRSC RVCSNRHGLI RKYGLNMCRQ CFRQYAKDIG FIKLD

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #12: Receptor of activated protein C kinase 1

MacromoleculeName: Receptor of activated protein C kinase 1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.669113 KDa
SequenceString: TEQMTLRGTL KGHNGWVTQI ATTPQFPDMI LSASRDKTII MWKLTRDETN YGIPQRALRG HSHFVSDVVI SSDGQFALSG SWDGTLRLW DLTTGTTTRR FVGHTKDVLS VAFSSDNRQI VSGSRDKTIK LWNTLGVCKY TVQDESHSEW VSCVRFSPNS S NPIIVSCG ...String:
TEQMTLRGTL KGHNGWVTQI ATTPQFPDMI LSASRDKTII MWKLTRDETN YGIPQRALRG HSHFVSDVVI SSDGQFALSG SWDGTLRLW DLTTGTTTRR FVGHTKDVLS VAFSSDNRQI VSGSRDKTIK LWNTLGVCKY TVQDESHSEW VSCVRFSPNS S NPIIVSCG WDKLVKVWNL ANCKLKTNHI GHTGYLNTVT VSPDGSLCAS GGKDGQAMLW DLNEGKHLYT LDGGDIINAL CF SPNRYWL CAATGPSIKI WDLEGKIIVD ELKQEVISTS SKAEPPQCTS LAWSADGQTL FAGYTDNLVR VWQVTI

UniProtKB: Small ribosomal subunit protein RACK1

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Macromolecule #13: Small ribosomal subunit protein eS12

MacromoleculeName: Small ribosomal subunit protein eS12 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.652019 KDa
SequenceString:
VMDVNTALQE VLKTALIHDG LARGIREAAK ALDKRQAHLC VLASNCDEPM YVKLVEALCA EHQINLIKVD DNKKLGEWVG LCKIDREGK PRKVVGCSCV VVKDYGKESQ AKDVIEEYFK CKK

UniProtKB: Small ribosomal subunit protein eS12

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Macromolecule #14: Small ribosomal subunit protein eS25

MacromoleculeName: Small ribosomal subunit protein eS25 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.526119 KDa
SequenceString:
RDKLNNLVLF DKATYDKLCK EVPNYKLITP AVVSERLKIR GSLARAALQE LLSKGLIKLV SKHRAQVIYT RNTKG

UniProtKB: Small ribosomal subunit protein eS25

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Macromolecule #15: Ubiquitin-40S ribosomal protein S27a

MacromoleculeName: Ubiquitin-40S ribosomal protein S27a / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.884286 KDa
SequenceString:
YTTPKKNKHK RKKVKLAVLK YYKVDENGKI SRLRRECPSD ECGAGVFMAS HFDRHYCGKC CLTYCFN

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #16: 18S rRNA

MacromoleculeName: 18S rRNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 561.332438 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC CACUUGGAUA ACUGUGGUAA U UCUAGAGC ...String:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUGGUUCCU UUGGUCGCUC GCUCCUCUCC CACUUGGAUA ACUGUGGUAA U UCUAGAGC UAAUACAUGC CGACGGGCGC UGACCCCCUU CGCGGGGGGG AUGCGUGCAU UUAUCAGUGG UGACUCUAGA UA ACCUCGG GCCGAUCGCA CGCCCCCCGU GGCGGCGACG ACCCAUUCGA ACGUCUGCCC UAUCAACUUU CGAUGGUAGU CGC CGUGCC UACCAUGGUG ACCACGGGUG ACGGGGAAUC AGGGUUCGAU UCCGGAGAGG GAGCCUGAGA AACGGCUACC ACAU CCAAG GAAGGCAGCA GGCGCGCAAA UUACCCACUC CCGACCCGGG GAGGUAGUGA CGAAAAAUAA CAAUACAGGA CUCUU UCGA GGCCCUGUAA UUGGAAUGAG UCCACUUUAA AUCCUUUAAC GAGGAUCCAU UGGAGGGCAA GUCUGGUGCC AGCAGC CGC GGUAAUUCCA GCUCCAAUAG CGUAUAUUAA AGUUGCUGCA GUUAAAAAGC UCGUAGUUGG AUCUUGGGAG CGGGCGU CC CCGCCCUCUC GGCCGGGGCC CGAAGCGUUU ACUUUGAAAA AAUUAGAGUG UUCAAAGCAG GCCCGAGCCG CCUGGAUA C CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGG CCGGGGGCAU UCGUAUUGCG CCGCUAGAGG UGAAAUUCUU GGACCGGCGC AAGACGGACC AGAGCGAAAG CAUUUGCCAA GAAUGUUUU CAUUAAUCAA GAACGAAAGU CGGAGGUUCG AAGACGAUCA GAUACCGUCG UAGUUCCGAC CAUAAACGAU G CCGACCGG CGAUGCGGCG GCGUUAUUCC CAUGACCCGC CGGGCAGCUU CCGGGAAACC AAAGUCUUUG GGUUCCGGGG GG AGUAUGG UUGCAAAGCU GAAACUUAAA GGAAUUGACG GAAGGGCACC ACCAGGAGUG GAGCCUGCGG CUUAAUUUGA CUC AACACG GGAAACCUCA CCCGGCCCGG ACACGGACAG GAUUGACAGA UUGAUAGCUC UUUCUCGAUU CCGUGGGUGG UGGU GCAUG GCCGUUCUUA GUUGGUGGAG CGAUUUGUCU GGUUAAUUCC GAUAACGAAC GAGACUCUGG CAUGCUAACU AGUUA CGCG ACCCCCGAGC GGUCGGCGUC CCCCAACUUC UUAGAGGGAC AAGUGGCGUU CAGCCACCCG AGAUUGAGCA AUAACA GGU CUGUGAUGCC CUUAGAUGUC CGGGGCUGCA CGCGCGCUAC ACUGACUGGC UCAGCGUGUG CCUACCCUAC GCCGGCA GG CGCGGGUAAC CCGUUGAACC CCAUUCGUGA UGGGGAUCGG GGAUUGCAAU UAUUCCCCAU GAACGAGGAA UUCCCAGU A AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUU UAGUGAGGCC CUCGGAUCGG CCCCGCCGGG GUCGGCCCAC GGCCCUGGCG GAGCGCUGAG AAGACGGUCG AACUUGACUA UCUAGAGGA AGUAAAAGUC GUAACAAGGU UUCCGUAGGU GAACCUGCGG AAGGAUCAUU A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1754680
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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About Yorodumi

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