PDB-9but: Single particle CryoEM structure of the Pf80S ribosome in the rot...

ID or keywords:

Entry

Database: PDB / ID: 9but

Title

Single particle CryoEM structure of the Pf80S ribosome in the rotated-2 PRE state (rt state with P and E-site tRNA)

Components

(40S ribosomal protein ...) x 31
(60S ribosomal protein ...) x 37
(Large ribosomal subunit protein ...) x 2
(Ribosomal protein ...) x 2
18S ribosomal RNA
28S ribosomal RNA
5.8S ribosomal RNA
5S ribosomal RNA
Ubiquitin-60S ribosomal protein L40
mRNA
tRNA

Keywords

RIBOSOME / malaria / single particle / translation

Function / homology

Function and homology information

RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs ...RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision 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 / Translation initiation complex formation / 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 / Negative regulators of DDX58/IFIH1 signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / PINK1-PRKN Mediated Mitophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Aggrephagy / 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 / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / ubiquitin-dependent protein catabolic process / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function

: / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...: / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S7e / Ribosomal protein L39e, conserved site / Ribosomal protein S7e / Ribosomal protein L39e signature. / 40S ribosomal protein S1/3, eukaryotes / : / Ribosomal protein S19A/S15e / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S17e
Similarity search - Domain/homology

: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 / 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 / 60S ribosomal protein L4 / 60S ribosomal protein L31 / 40S ribosomal protein S17, putative / 60S ribosomal protein L36 / 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 / 60S ribosomal protein L17, putative / 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 / 40S ribosomal protein S20e, putative / 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
Similarity search - Component

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å

Authors

Anton, L. / Haile, M. / Ho, C.M.

Funding support

United States,

Switzerland,

France, 3items

Organization	Grant number	Country
National Institutes of Health/Office of the Director	DP5OD029613	United States
Swiss National Science Foundation	P2BSP3_200205	Switzerland
Human Frontier Science Program (HFSP)	LT000452/2021-L	France

Citation

Journal: To Be Published
Title: Inhibiting elongation factor binding to the malarial 80S ribosome triggers ribosome biogenesis
Authors: Anton, L. / Cheng, W. / Haile, M. / Cobb, D.W. / Zhu, X. / Han, L. / Li, E. / Nair, A. / Lee, C.L. / Ho, C.M.

History

Deposition	May 17, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	May 28, 2025	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9but.cif.gz	5.7 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	9but_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9but_full_validation.pdf.gz	2.6 MB	Display
Data in XML	9but_validation.xml.gz	394.6 KB	Display
Data in CIF	9but_validation.cif.gz	650 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bu/9but ftp://data.pdbj.org/pub/pdb/validation_reports/bu/9but	HTTPS FTP

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Related structure data

Related structure data	44919MC 44915C 44918C 44920C 9bupC 9busC 9buuC 8tpu M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (68) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (3) #10 - Oct 2000 Ribosome similarity (69) #260 - Aug 2021 Ribonuclease P similarity (5) #253 - Jan 2021 Expressome similarity (3) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #161 - May 2013 Ricin similarity (205) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (93) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

S7: tRNA

AA: 28S ribosomal RNA

AC: 5.8S ribosomal RNA

AB: 5S ribosomal RNA

AL: 60S ribosomal protein L13

A1: 60S ribosomal protein L27

A2: 60S ribosomal protein L28

A4: 60S ribosomal protein L29

A6: 60S ribosomal protein L30e

A7: 60S ribosomal protein L31

AN: 60S ribosomal protein L14

A8: 60S ribosomal protein L32

A9: 60S ribosomal protein L35ae

Aa: 60S ribosomal protein L34

Ab: 60S ribosomal protein L36

Ad: 60S ribosomal protein L38

Ae: 60S ribosomal protein L39

Af: Ubiquitin-60S ribosomal protein L40

AP: Ribosomal protein L15

Ah: Large ribosomal subunit protein eL43

Ai: Large ribosomal subunit protein eL42

AI: 60S ribosomal protein L6

AJ: 60S ribosomal protein L7a

Ac: Ribosomal protein L37

AK: 60S ribosomal protein L13

AM: 60S ribosomal protein L23

AS: 60S ribosomal protein L18-2

AO: 60S ribosomal protein L27a

AQ: 60S ribosomal protein L10

AR: 60S ribosomal protein L5

AW: 60S ribosomal protein L17

AY: 60S ribosomal protein L23

AT: 60S ribosomal protein L19

AZ: 60S ribosomal protein L26

A3: 60S ribosomal protein L35

A5: 60S ribosomal protein L7

AD: 60S ribosomal protein L2

AE: 60S ribosomal protein L3

AF: 60S ribosomal protein L4

AG: 60S ribosomal protein L11a

AU: 60S ribosomal protein L18a

AH: 60S ribosomal protein L6

AV: 60S ribosomal protein L21

Ag: 60S ribosomal protein L41

AX: 60S ribosomal protein L22

A0: 60S ribosomal protein L24

S1: 40S ribosomal protein S24

S2: 40S ribosomal protein S25

S3: 40S ribosomal protein S26

S4: 40S ribosomal protein S27

S5: 40S ribosomal protein S28e

S6: 40S ribosomal protein S30

SA: 18S ribosomal RNA

SB: 40S ribosomal protein S3a

SC: 40S ribosomal protein SA

SD: 40S ribosomal protein S3

SE: 40S ribosomal protein S9

SF: 40S ribosomal protein S4

SG: 40S ribosomal protein S5

SH: 40S ribosomal protein S6

SI: 40S ribosomal protein S5

SJ: 40S ribosomal protein S7

SK: 40S ribosomal protein S15A

SL: 40S ribosomal protein S8

SM: 40S ribosomal protein S16

SN: 40S ribosomal protein S20e

SO: 40S ribosomal protein S10

SP: 40S ribosomal protein S11

SQ: 40S ribosomal protein S23

SR: 40S ribosomal protein S12

SS: 40S ribosomal protein S18

ST: 40S ribosomal protein S29

SU: 40S ribosomal protein S15

SV: 40S ribosomal protein S11

SW: 40S ribosomal protein S17

SX: 40S ribosomal protein S19

SY: 40S ribosomal protein S19

SZ: 40S ribosomal protein S21

mR: mRNA

S9: tRNA

3.42 MDa, 80 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: electron microscopy, not applicable

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RNA chain , 6 types, 7 molecules S7S9AAACABSAmR

#1: RNA chain	tRNA Mass: 24496.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1870104878
#2: RNA chain	28S ribosomal RNA Mass: 1216213.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1013064538
#3: 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: 1162436939
#4: RNA chain	5S ribosomal RNA Mass: 38346.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1016052399
#53: 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) / References: GenBank: 1013064403
#79: RNA chain	mRNA Mass: 2710.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)

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60S ribosomal protein ... , 37 types, 37 molecules ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5ADAEAF...

#5: 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
#6: 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
#7: 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
#8: 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
#9: Protein	60S ribosomal protein L30e Mass: 11794.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJK8
#10: 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
#11: Protein	60S ribosomal protein L14 Mass: 19340.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILE8
#12: 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
#13: Protein	60S ribosomal protein L35ae Mass: 16306.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHT9
#14: 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
#15: 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
#16: 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
#17: 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
#22: Protein	60S ribosomal protein L6 Mass: 25587.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: A0A5K1K8V8
#23: 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
#25: Protein	60S ribosomal protein L13 Mass: 23805.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJZ7
#26: Protein	60S ribosomal protein L23 Mass: 15015.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE09
#27: Protein	60S ribosomal protein L18-2 Mass: 21508.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H5G3
#28: Protein	60S ribosomal protein L27a Mass: 16765.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6KT23
#29: Protein	60S ribosomal protein L10 Mass: 25265.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILV2
#30: Protein	60S ribosomal protein L5 Mass: 34067.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILL3
#31: Protein	60S ribosomal protein L17 Mass: 19431.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDI5
#32: 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
#33: 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
#34: Protein	60S ribosomal protein L26 Mass: 14855.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77364
#35: Protein	60S ribosomal protein L35 Mass: 14787.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIB4
#36: Protein	60S ribosomal protein L7 Mass: 30593.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97250
#37: 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
#38: 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
#39: 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
#40: Protein	60S ribosomal protein L11a Mass: 20268.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBQ6
#41: 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
#42: Protein	60S ribosomal protein L6 Mass: 21638.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE85
#43: 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
#44: 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
#45: Protein	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
#46: Protein	60S ribosomal protein L24 Mass: 19295.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IEM3

-
Protein , 1 types, 1 molecules Af

#18: 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

-
Ribosomal protein ... , 2 types, 2 molecules APAc

#19: 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
#24: 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

-
Large ribosomal subunit protein ... , 2 types, 2 molecules AhAi

#20: 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
#21: 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

+
40S ribosomal protein ... , 31 types, 31 molecules S1S2S3S4S5S6SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ

#47: 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
#48: 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
#49: 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
#50: 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
#51: Protein	40S ribosomal protein S28e Mass: 7508.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IKL9
#52: Protein	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
#54: Protein	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
#55: Protein	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
#56: 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
#57: Protein	40S ribosomal protein S9 Mass: 22172.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3R0
#58: 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
#59: 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
#60: 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
#61: Protein	40S ribosomal protein S5 Mass: 21898.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBN5
#62: 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
#63: Protein	40S ribosomal protein S15A Mass: 14900.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77395
#64: 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
#65: Protein	40S ribosomal protein S16 Mass: 16318.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: A0A0L7M7C8
#66: Protein	40S ribosomal protein S20e Mass: 13534.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IK02
#67: Protein	40S ribosomal protein S10 Mass: 16510.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBQ5
#68: 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
#69: Protein	40S ribosomal protein S23 Mass: 16166.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97248
#70: Protein	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
#71: Protein	40S ribosomal protein S18 Mass: 17928.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIA2
#72: Protein	40S ribosomal protein S29 Mass: 6430.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4K8
#73: 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
#74: Protein	40S ribosomal protein S11 Mass: 18801.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77381
#75: Protein	40S ribosomal protein S17 Mass: 16096.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I502
#76: 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
#77: 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
#78: 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

-
Details

Has protein modification	Y

-
Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: CELL / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component	Name: Plasmodium falciparum 80S ribosome in non-rotated state with E-site tRNA Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weight	Value: 4 MDa / Experimental value: NO
Source (natural)	Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recording	Electron dose: 60 e/Å² / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software

Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement

CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

3D reconstruction

Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69147 / Symmetry type: POINT

Refinement

Cross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

Displacement parameters

B_iso mean: 121.01 Å²

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
ELECTRON MICROSCOPY	f_bond_d	0.0025	209459
ELECTRON MICROSCOPY	f_angle_d	0.6209	307369
ELECTRON MICROSCOPY	f_chiral_restr	0.0349	38587
ELECTRON MICROSCOPY	f_plane_restr	0.0047	19446
ELECTRON MICROSCOPY	f_dihedral_angle_d	22.0793	85198

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RNA chain , 6 types, 7 molecules S7S9AAACABSAmR

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60S ribosomal protein ... , 37 types, 37 molecules ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5ADAEAF...

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Protein , 1 types, 1 molecules Af

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Ribosomal protein ... , 2 types, 2 molecules APAc

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Large ribosomal subunit protein ... , 2 types, 2 molecules AhAi

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40S ribosomal protein ... , 31 types, 31 molecules S1S2S3S4S5S6SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ

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+60S ribosomal protein ... , 37 types, 37 molecules ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5ADAEAF...

-Protein , 1 types, 1 molecules Af

-Ribosomal protein ... , 2 types, 2 molecules APAc

-Large ribosomal subunit protein ... , 2 types, 2 molecules AhAi

+40S ribosomal protein ... , 31 types, 31 molecules S1S2S3S4S5S6SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ

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RNA chain , 6 types, 7 molecules S7S9AAACABSAmR

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60S ribosomal protein ... , 37 types, 37 molecules ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5ADAEAF...

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Protein , 1 types, 1 molecules Af

-
Ribosomal protein ... , 2 types, 2 molecules APAc

-
Large ribosomal subunit protein ... , 2 types, 2 molecules AhAi

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40S ribosomal protein ... , 31 types, 31 molecules S1S2S3S4S5S6SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ

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Experimental details

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