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- PDB-9j9i: High-resolution cryo-EM structure of the Plasmodium falciparum 80... -

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Basic information

Entry
Database: PDB / ID: 9j9i
TitleHigh-resolution cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to E-tRNA
Components
  • (40S ribosomal protein ...) x 27
  • (60S ribosomal protein ...) x 36
  • (Large ribosomal subunit protein ...) x 3
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 4
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin-60S ribosomal protein L40
  • tRNA
KeywordsRIBOSOME / Plasmodium falciparum
Function / homology
Function and homology information


: / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Regulation of TNFR1 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death ...: / RMTs methylate histone arginines / Protein methylation / Protein hydroxylation / Translesion synthesis by REV1 / Translesion Synthesis by POLH / Regulation of TNFR1 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / Josephin domain DUBs / Ovarian tumor domain proteases / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Aggrephagy / SCF-beta-TrCP mediated degradation of Emi1 / Degradation of DVL / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / AUF1 (hnRNP D0) binds and destabilizes mRNA / ABC-family protein mediated transport / preribosome / protein neddylation / regulation of proteolysis / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / protein-RNA complex assembly / 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) / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / chloroplast / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. ...: / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L6e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L7A/L8 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L30/YlxQ
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L6, putative / 40S ribosomal protein S11 / Ribosomal protein L15 / 60S ribosomal protein L39 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L6, putative / 40S ribosomal protein S11 / Ribosomal protein L15 / 60S ribosomal protein L39 / 40S ribosomal protein S29, putative / Ribosomal protein L37 / 40S ribosomal protein S19 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 / 60S ribosomal protein L29 / 60S ribosomal protein L26, putative / 40S ribosomal protein S11, putative / 40S ribosomal protein S15A, putative / Large ribosomal subunit protein eL43 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS30 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS12 / 60S ribosomal protein L7, putative / Small ribosomal subunit protein eS1 / 60S ribosomal protein L32 / 40S ribosomal protein S9, putative / 40S ribosomal protein S24 / 60S ribosomal protein L2 / Large ribosomal subunit protein uL4 / 60S ribosomal protein L31 / 40S ribosomal protein S17, putative / 60S ribosomal protein L36 / 40S ribosomal protein S16, putative / 60S ribosomal protein L13 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S5, putative / 40S ribosomal protein S10, putative / 60S ribosomal protein L11a, putative / 60S ribosomal protein L34 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S15 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S6 / 60S ribosomal protein L18a / 60S ribosomal protein L23, putative / 60S ribosomal protein L23 / 60S ribosomal protein L6, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 60S ribosomal protein L35ae, putative / 60S ribosomal protein L28 / 60S ribosomal protein L38 / 40S ribosomal protein S18, putative / 60S ribosomal protein L35, putative / 40S ribosomal protein S4 / 60S ribosomal protein L3 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L30e, putative / 60S ribosomal protein L13, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / 60S ribosomal protein L27 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L14, putative / 60S ribosomal protein L21 / 60S ribosomal protein L7a / 60S ribosomal protein L5, putative / 40S ribosomal protein S25 / 60S ribosomal protein L10, putative / 40S ribosomal protein S8 / Ribosomal protein S27a, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsYan, X.F. / Gao, Y.G.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE-T2EP30122-0019 Singapore
Ministry of Education (MoE, Singapore)RG108/20 Singapore
CitationJournal: Structure / Year: 2025
Title: Antimalarial drug artemisinin stabilizes PfRACK1 binding to the ribosome.
Authors: Ka Diam Go / Xin-Fu Yan / Grennady Wirjanata / Rya Ero / Samuel Pazicky / Jerzy Dziekan / Seth Tjia / Julien Lescar / Zbynek Bozdech / Yong-Gui Gao /
Abstract: Artemisinin and its derivatives represent the core agents in artemisinin combination therapies that are the current frontline treatment for P. falciparum and P. vivax malaria infections. Artemisinins ...Artemisinin and its derivatives represent the core agents in artemisinin combination therapies that are the current frontline treatment for P. falciparum and P. vivax malaria infections. Artemisinins are known to bind a wide array of proteins that disrupt the parasite's cellular physiology. Here, we show that artemisinins' cytotoxic activity involves structural alteration of key P. falciparum macromolecular complexes, including the ribosome, proteasome, and T-complex. The structural analysis revealed that, following artemisinin treatment, a larger population of Pf80S ribosomes binds PfRACK1. Unlike in most eukaryotes, PfRACK1 does not interact with the C-terminal tail of the r-protein uS3 that in Plasmodium is truncated. This likely suggests an evolved role of uS3 in facilitating RACK1-mediated translational regulation, which would potentially benefit the parasite under certain conditions. Stabilization of RACK1 ribosome interaction likely contributes to artemisinins' mode of action.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Aug 27, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 28S ribosomal RNA
AA: Small ribosomal subunit protein eS12
j: 18S ribosomal RNA
AH: 40S ribosomal protein S19
B: 5S ribosomal RNA
AB: 40S ribosomal protein S18, putative
k: Small ribosomal subunit protein eS1
C: 5.8S ribosomal RNA
AC: 40S ribosomal protein S29, putative
l: Small ribosomal subunit protein uS2
D: 60S ribosomal protein L2
0: 60S ribosomal protein L24, putative
n: 40S ribosomal protein S9, putative
E: 60S ribosomal protein L3
1: 60S ribosomal protein L27
o: 40S ribosomal protein S4
F: 60S ribosomal protein L4
2: 60S ribosomal protein L28
p: 40S ribosomal protein S5
G: 60S ribosomal protein L11a, putative
3: 60S ribosomal protein L35, putative
q: 40S ribosomal protein S6
H: 60S ribosomal protein L6, putative
4: 60S ribosomal protein L29
s: 40S ribosomal protein S7
I: 60S ribosomal protein L6, putative
5: 60S ribosomal protein L7, putative
t: 40S ribosomal protein S15A, putative
J: 60S ribosomal protein L7a
6: 60S ribosomal protein L30e, putative
u: 40S ribosomal protein S8
K: 60S ribosomal protein L13, putative
7: 60S ribosomal protein L31
y: 40S ribosomal protein S11
L: 60S ribosomal protein L13
8: 60S ribosomal protein L32
z: 40S ribosomal protein S23, putative
M: 60S ribosomal protein L23, putative
9: 60S ribosomal protein L35ae, putative
AD: 40S ribosomal protein S15
N: 60S ribosomal protein L14, putative
a: 60S ribosomal protein L34
AE: 40S ribosomal protein S11, putative
O: 60S ribosomal protein L27a, putative
b: 60S ribosomal protein L36
AI: 40S ribosomal protein S21
P: Ribosomal protein L15
c: Ribosomal protein L37
AQ: tRNA
Q: 60S ribosomal protein L10, putative
d: 60S ribosomal protein L38
AK: 40S ribosomal protein S25
R: 60S ribosomal protein L5, putative
e: 60S ribosomal protein L39
AN: 40S ribosomal protein S28e, putative
S: 60S ribosomal protein L18-2, putative
f: Ubiquitin-60S ribosomal protein L40
AP: Ribosomal protein S27a, putative
T: 60S ribosomal protein L19
g: 60S ribosomal protein L41
m: 40S ribosomal protein S3
U: 60S ribosomal protein L18a
h: Large ribosomal subunit protein eL43
r: 40S ribosomal protein S5, putative
V: 60S ribosomal protein L21
i: Large ribosomal subunit protein eL42
v: 40S ribosomal protein S16, putative
W: 60S ribosomal protein L17, putative
AJ: 40S ribosomal protein S24
w: 40S ribosomal protein S20e, putative
X: Large ribosomal subunit protein eL22
AL: 40S ribosomal protein S26
x: 40S ribosomal protein S10, putative
Y: 60S ribosomal protein L23
AM: 40S ribosomal protein S27
AF: 40S ribosomal protein S17, putative
Z: 60S ribosomal protein L26, putative
AO: Small ribosomal subunit protein eS30
AG: 40S ribosomal protein S19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,416,818339
Polymers3,410,25279
Non-polymers6,566260
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules AjBCAQ

#1: RNA chain 28S ribosomal RNA


Mass: 1216541.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#3: RNA chain 18S ribosomal RNA


Mass: 671337.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#5: RNA chain 5S ribosomal RNA


Mass: 38410.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#8: RNA chain 5.8S ribosomal RNA


Mass: 51206.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1060141538
#49: RNA chain tRNA


Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1060142279

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Small ribosomal subunit protein ... , 4 types, 4 molecules AAklAO

#2: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 15414.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97249
#7: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a


Mass: 30111.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97313
#10: Protein Small ribosomal subunit protein uS2 / 40S ribosomal protein S2 / 40S ribosomal protein SA


Mass: 29891.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJD4
#78: Protein Small ribosomal subunit protein eS30 / 40S ribosomal protein S30


Mass: 6508.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96269

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40S ribosomal protein ... , 27 types, 27 molecules AHABACnopqstuyzADAEAIAKANmrvAJwALxAMAFAG

#4: Protein 40S ribosomal protein S19


Mass: 19757.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IFP2
#6: Protein 40S ribosomal protein S18, putative


Mass: 17928.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIA2
#9: Protein 40S ribosomal protein S29, putative


Mass: 6430.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4K8
#13: Protein 40S ribosomal protein S9, putative


Mass: 22172.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3R0
#16: Protein 40S ribosomal protein S4


Mass: 29830.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIU8
#19: Protein 40S ribosomal protein S5


Mass: 30008.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IL02
#22: Protein 40S ribosomal protein S6


Mass: 35473.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDR9
#25: Protein 40S ribosomal protein S7


Mass: 22524.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IET7
#28: Protein 40S ribosomal protein S15A, putative


Mass: 14900.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77395
#31: Protein 40S ribosomal protein S8


Mass: 25105.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IM10
#34: Protein 40S ribosomal protein S11


Mass: 16105.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: A0A5K1K925
#37: Protein 40S ribosomal protein S23, putative


Mass: 16166.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97248
#40: Protein 40S ribosomal protein S15


Mass: 17286.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDB0
#43: Protein 40S ribosomal protein S11, putative


Mass: 18801.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77381
#46: Protein 40S ribosomal protein S21


Mass: 9157.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHS5
#52: Protein 40S ribosomal protein S25


Mass: 11691.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILN8
#55: Protein 40S ribosomal protein S28e, putative


Mass: 7508.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IKL9
#61: Protein 40S ribosomal protein S3


Mass: 24709.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IKH8
#64: Protein 40S ribosomal protein S5, putative


Mass: 21898.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBN5
#67: Protein 40S ribosomal protein S16, putative


Mass: 16318.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IAX5
#69: Protein 40S ribosomal protein S24


Mass: 15431.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3R6
#70: Protein 40S ribosomal protein S20e, putative


Mass: 13534.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IK02
#72: Protein 40S ribosomal protein S26


Mass: 12539.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96258
#73: Protein 40S ribosomal protein S10, putative


Mass: 16510.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBQ5
#75: Protein 40S ribosomal protein S27


Mass: 9154.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IEN2
#76: Protein 40S ribosomal protein S17, putative


Mass: 16096.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I502
#79: Protein 40S ribosomal protein S19


Mass: 16800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H5C2

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60S ribosomal protein ... , 36 types, 36 molecules D0E1F2G3H4I5J6K7L8M9NaObQdReST...

#11: Protein 60S ribosomal protein L2


Mass: 28064.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3T9
#12: Protein 60S ribosomal protein L24, putative


Mass: 19295.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IEM3
#14: Protein 60S ribosomal protein L3


Mass: 44318.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJC6
#15: Protein 60S ribosomal protein L27


Mass: 16785.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IKM5
#17: Protein 60S ribosomal protein L4


Mass: 46311.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I431
#18: Protein 60S ribosomal protein L28


Mass: 14437.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHU0
#20: Protein 60S ribosomal protein L11a, putative


Mass: 20268.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBQ6
#21: Protein 60S ribosomal protein L35, putative


Mass: 14787.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIB4
#23: Protein 60S ribosomal protein L6, putative


Mass: 21638.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE85
#24: Protein 60S ribosomal protein L29


Mass: 8041.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6S3J6
#26: Protein 60S ribosomal protein L6, putative


Mass: 25587.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: A0A5K1K8V8
#27: Protein 60S ribosomal protein L7, putative


Mass: 30593.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97250
#29: Protein 60S ribosomal protein L7a


Mass: 32760.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILL2
#30: Protein 60S ribosomal protein L30e, putative


Mass: 11794.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJK8
#32: Protein 60S ribosomal protein L13, putative


Mass: 23805.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJZ7
#33: Protein 60S ribosomal protein L31


Mass: 14099.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I463
#35: Protein 60S ribosomal protein L13


Mass: 25508.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IAX6
#36: Protein 60S ribosomal protein L32


Mass: 15565.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3B0
#38: Protein 60S ribosomal protein L23, putative


Mass: 15015.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE09
#39: Protein 60S ribosomal protein L35ae, putative


Mass: 16306.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHT9
#41: Protein 60S ribosomal protein L14, putative


Mass: 19340.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILE8
#42: Protein 60S ribosomal protein L34


Mass: 17406.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBY4
#44: Protein 60S ribosomal protein L27a, putative


Mass: 16765.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6KT23
#45: Protein 60S ribosomal protein L36


Mass: 12825.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I713
#50: Protein 60S ribosomal protein L10, putative


Mass: 25265.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILV2
#51: Protein 60S ribosomal protein L38


Mass: 10341.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8II62
#53: Protein 60S ribosomal protein L5, putative


Mass: 34067.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILL3
#54: Protein 60S ribosomal protein L39


Mass: 6540.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4H3
#56: Protein 60S ribosomal protein L18-2, putative


Mass: 21508.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H5G3
#59: Protein 60S ribosomal protein L19


Mass: 21641.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6KSY6
#60: Protein/peptide 60S ribosomal protein L41


Mass: 5108.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6S3G4
#62: Protein 60S ribosomal protein L18a


Mass: 21793.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDS6
#65: Protein 60S ribosomal protein L21


Mass: 18840.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILK3
#68: Protein 60S ribosomal protein L17, putative


Mass: 23469.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDI5
#74: Protein 60S ribosomal protein L23


Mass: 22152.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE82
#77: Protein 60S ribosomal protein L26, putative


Mass: 14855.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77364

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Ribosomal protein ... , 3 types, 3 molecules PcAP

#47: Protein Ribosomal protein L15


Mass: 24197.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4A6
#48: Protein Ribosomal protein L37


Mass: 10571.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4L5
#58: Protein Ribosomal protein S27a, putative


Mass: 17437.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IM64

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Protein , 1 types, 1 molecules f

#57: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14645.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ID50

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Large ribosomal subunit protein ... , 3 types, 3 molecules hiX

#63: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10826.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96184
#66: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L44


Mass: 12194.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97231
#71: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 16422.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IB51

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Non-polymers , 2 types, 260 molecules

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


Mass: 24.305 Da / Num. of mol.: 254 / Source method: obtained synthetically / Formula: Mg
#81: Chemical
ChemComp-ZN / ZINC ION


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

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Plasmodium falciparum cytoplasmic ribosomes / Type: RIBOSOME / Entity ID: #1-#26, #30-#76, #27-#29, #77-#79 / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85400 / Symmetry type: POINT

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