EMDB-11440: Human RIO1(kd)-StHA late pre-40S particle, structural state A (pr...

Basic information

• Entry: Database: EMDB / ID: EMD-11440
• Title: Human RIO1(kd)-StHA late pre-40S particle, structural state A (pre 18S rRNA cleavage)

Sample

human cytoplasmic late precursor to the small ribosomal subunit, purified using RIO1(kd)-StHA as bait. Structural state A (pre 18S rRNA maturation)

• nucleic-acidNucleic acid
• (40S ribosomal protein ...) x 30
• Ubiquitin-40S ribosomal protein S27a
• Receptor of activated protein C kinase 1
• (RNA-binding protein ...) x 2
• ligand

Function / homology

Function:

cleavage involved in rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / mammalian oogenesis stage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / cytoplasmic side of rough endoplasmic reticulum membrane / TNFR1-mediated ceramide production / laminin receptor activity / rRNA modification in the nucleus and cytosol / regulation of cell division / activation-induced cell death of T cells / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / negative regulation of ubiquitin protein ligase activity / positive regulation of ceramide biosynthetic process / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / erythrocyte homeostasis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of phagocytosis / NF-kappaB complex / regulation of establishment of cell polarity / signaling adaptor activity / negative regulation of Wnt signaling pathway / positive regulation of endodeoxyribonuclease activity / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of mitochondrial depolarization / translation regulator activity / supercoiled DNA binding / protein kinase A binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phagocytic cup / ion channel inhibitor activity / positive regulation of apoptotic signaling pathway / preribosome, small subunit precursor / negative regulation of smoothened signaling pathway / erythrocyte development / TOR signaling / iron-sulfur cluster binding / ubiquitin-like protein conjugating enzyme binding / Peptide chain elongation / Ribosomal scanning and start codon recognition / positive regulation of cellular component movement / Selenocysteine synthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / fibroblast growth factor binding / rescue of stalled ribosome / mTORC1-mediated signalling / Formation of a pool of free 40S subunits / Translation initiation complex formation / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / T cell proliferation involved in immune response / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / Viral mRNA Translation / positive regulation of activated T cell proliferation / GTP hydrolysis and joining of the 60S ribosomal subunit / GABA-ergic synapse / positive regulation of cyclic-nucleotide phosphodiesterase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of T cell receptor signaling pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / Protein methylation / gastrulation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / spindle assembly / small-subunit processome / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase

Domain/homology:

Nin one binding (NOB1) Zn-ribbon-like / Ribonuclease Nob1, eukaryote / Nin one binding (NOB1) Zn-ribbon like / Putative WW-binding domain and destruction box / NOB1 zinc finger-like superfamily / Putative WW-binding domain and destruction box / RNA-binding protein NOB1 / Ribonuclease, PIN domain / PIN domain of ribonuclease / Pre-rRNA-processing protein PNO1-like / Large family of predicted nucleotide-binding domains / PIN domain / 40S ribosomal protein SA / 40S ribosomal protein SA C-terminus / 40S ribosomal protein SA, C-terminal domain / Ribosomal protein S8e subdomain, eukaryotes / K Homology domain, type 1 superfamily / Ribosomal protein S21e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S2, eukaryotic / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein S12e signature. / Ribosomal protein S19e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S12e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S25 / S25 ribosomal protein / Plectin/S10 domain / Plectin/S10, N-terminal / Ribosomal_S19e / Ribosomal protein S19e / : / Ribosomal protein S19e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S17e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S17e / Ribosomal protein S27e signature. / Ribosomal protein S7e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4e / Ribosomal family S4e / Ribosomal protein S4e, central region / Ribosomal protein S4, KOW domain / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S24e / Ribosomal protein S6, eukaryotic / Ribosomal protein S24e / Ribosomal protein S3Ae signature. / Ribosomal protein S3Ae, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S23, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S6e signature. / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S15P / Ribosomal protein S28e signature. / Ribosomal protein S28e conserved site / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2

Component:

40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S24 / 40S ribosomal protein S25 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 40S ribosomal protein S23 / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / RNA-binding protein PNO1 / 40S ribosomal protein S18 / 40S ribosomal protein S7 / 40S ribosomal protein S14 / 40S ribosomal protein S27 / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 40S ribosomal protein S9 / 40S ribosomal protein S16 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S8 / 40S ribosomal protein S15a / RNA-binding protein NOB1

• Biological species: Homo sapiens (human) / Human (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.1 Å
• Authors: Plassart L / Shayan R / Plisson-Chastang C

Funding support

France, 1 items

Organization	Grant number	Country
French National Research Agency	ANR 16-CE11-0029	France

• Citation: Journal: Elife / Year: 2021; Title: The final step of 40S ribosomal subunit maturation is controlled by a dual key lock.; Authors: Laura Plassart / Ramtin Shayan / Christian Montellese / Dana Rinaldi / Natacha Larburu / Carole Pichereaux / Carine Froment / Simon Lebaron / Marie-Françoise O'Donohue / Ulrike Kutay / Julien Marcoux / Pierre-Emmanuel Gleizes / Celia Plisson-Chastang / ; Abstract: Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.

History

Deposition	Jul 23, 2020	-
Header (metadata) release	May 12, 2021	-
Map release	May 12, 2021	-
Update	May 12, 2021	-
Current status	May 12, 2021	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11440.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.04 Å

Density

Contour Level	By AUTHOR: 0.0045 / Movie #1: 0.0045
Minimum - Maximum	-0.030198384 - 0.05852886
Average (Standard dev.)	3.2952983e-05 (±0.0016777217)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 399.36 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.04	1.04	1.04
M x/y/z	384	384	384
origin x/y/z	0.000	0.000	0.000
length x/y/z	399.360	399.360	399.360
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	384	384	384
D min/max/mean	-0.030	0.059	0.000

Supplemental data

Sample components

Entire human cytoplasmic late precursor to the small ribosomal subunit, ...

• Entire: Name: human cytoplasmic late precursor to the small ribosomal subunit, purified using RIO1(kd)-StHA as bait. Structural state A (pre 18S rRNA maturation); Number of components: 37

Component #1: protein, human cytoplasmic late precursor to the small ribosomal ...

• Protein: Name: human cytoplasmic late precursor to the small ribosomal subunit, purified using RIO1(kd)-StHA as bait. Structural state A (pre 18S rRNA maturation); Recombinant expression: No
• Mass: Theoretical: 1.4 MDa
• Source: Species: Homo sapiens (human) / Strain: HEK 293

Component #2: nucleic-acid, pre-18S ribosomal RNA

nucleic acid

Name: pre-18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCGCCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCCUGGCGG AGCGCUGAGA AGACGGUCGA ACUUGACUAU CUAGAGGAAG UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUAA

• Mass: Theoretical: 603.107062 kDa
• Source: Species: Homo sapiens (human)

Component #3: protein, 40S ribosomal protein SA

• Protein: Name: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 32.883938 kDa
• Source: Species: Human (human)

Component #4: protein, 40S ribosomal protein S3a

• Protein: Name: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 30.002061 kDa
• Source: Species: Human (human)

Component #5: protein, 40S ribosomal protein S2

• Protein: Name: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 31.376516 kDa
• Source: Species: Human (human)

Component #6: protein, 40S ribosomal protein S3

• Protein: Name: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 26.729369 kDa
• Source: Species: Human (human)

Component #7: protein, 40S ribosomal protein S4, X isoform

• Protein: Name: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 29.654869 kDa
• Source: Species: Human (human)

Component #8: protein, 40S ribosomal protein S5

• Protein: Name: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.913453 kDa
• Source: Species: Human (human)

Component #9: protein, 40S ribosomal protein S6

• Protein: Name: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.751906 kDa
• Source: Species: Human (human)

Component #10: protein, 40S ribosomal protein S7

• Protein: Name: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.168914 kDa
• Source: Species: Human (human)

Component #11: protein, 40S ribosomal protein S8

• Protein: Name: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 24.263387 kDa
• Source: Species: Human (human)

Component #12: protein, 40S ribosomal protein S9

• Protein: Name: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 22.641564 kDa
• Source: Species: Human (human)

Component #13: protein, 40S ribosomal protein S10

• Protein: Name: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.933846 kDa
• Source: Species: Human (human)

Component #14: protein, 40S ribosomal protein S11

• Protein: Name: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.468826 kDa
• Source: Species: Human (human)

Component #15: protein, 40S ribosomal protein S12

• Protein: Name: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.538987 kDa
• Source: Species: Human (human)

Component #16: protein, 40S ribosomal protein S13

• Protein: Name: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.259389 kDa
• Source: Species: Human (human)

Component #17: protein, 40S ribosomal protein S14

• Protein: Name: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.302772 kDa
• Source: Species: Human (human)

Component #18: protein, 40S ribosomal protein S15

• Protein: Name: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.076207 kDa
• Source: Species: Human (human)

Component #19: protein, 40S ribosomal protein S16

• Protein: Name: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.477377 kDa
• Source: Species: Human (human)

Component #20: protein, 40S ribosomal protein S17

• Protein: Name: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.578156 kDa
• Source: Species: Human (human)

Component #21: protein, 40S ribosomal protein S18

• Protein: Name: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.759777 kDa
• Source: Species: Human (human)

Component #22: protein, 40S ribosomal protein S19

• Protein: Name: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 16.091562 kDa
• Source: Species: Human (human)

Component #23: protein, 40S ribosomal protein S20

• Protein: Name: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 13.398763 kDa
• Source: Species: Human (human)

Component #24: protein, 40S ribosomal protein S21

• Protein: Name: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 9.124389 kDa
• Source: Species: Human (human)

Component #25: protein, 40S ribosomal protein S15a

• Protein: Name: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 14.865555 kDa
• Source: Species: Human (human)

Component #26: protein, 40S ribosomal protein S23

• Protein: Name: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.844666 kDa
• Source: Species: Human (human)

Component #27: protein, 40S ribosomal protein S24

• Protein: Name: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 15.463333 kDa
• Source: Species: Human (human)

Component #28: protein, 40S ribosomal protein S25

• Protein: Name: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 13.776224 kDa
• Source: Species: Human (human)

Component #29: protein, 40S ribosomal protein S27

• Protein: Name: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 9.480186 kDa
• Source: Species: Human (human)

Component #30: protein, 40S ribosomal protein S28

• Protein: Name: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 7.855052 kDa
• Source: Species: Human (human)

Component #31: protein, 40S ribosomal protein S29

• Protein: Name: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 6.690821 kDa
• Source: Species: Human (human)

Component #32: protein, 40S ribosomal protein S30

• Protein: Name: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 6.668938 kDa
• Source: Species: Human (human)

Component #33: protein, Ubiquitin-40S ribosomal protein S27a

• Protein: Name: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.004041 kDa
• Source: Species: Human (human)

Component #34: protein, Receptor of activated protein C kinase 1

• Protein: Name: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 35.115652 kDa
• Source: Species: Human (human)

Component #35: protein, RNA-binding protein PNO1

• Protein: Name: RNA-binding protein PNO1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 27.970355 kDa
• Source: Species: Human (human)

Component #36: protein, RNA-binding protein NOB1

• Protein: Name: RNA-binding protein NOB1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 46.743914 kDa
• Source: Species: Human (human)

Component #37: ligand, ZINC ION

• Ligand: Name: ZINC ION / Number of Copies: 3 / Recombinant expression: No
• Mass: Theoretical: 6.540905 MDa

Experimental details

Sample preparation

• Specimen: Specimen state: Particle / Method: cryo EM
• Sample solution: pH: 7.6
• Vitrification: Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 291 K / Humidity: 95 %

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 29.4 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: FEI TITAN KRIOS AUTOGRID HOLDER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

• Image acquisition: Number of digital images: 9494

Image processing

• Processing: Method: single particle reconstruction / Applied symmetry: C₁ (asymmetric) / Number of projections: 104844
• 3D reconstruction: Algorithm: EXACT BACK PROJECTION / Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Modeling #1

Refinement protocol: rigid body
Input PDB model: 6G51

6g51

Output model

6zuo