[English] 日本語
Yorodumi
- PDB-8tpu: Subtomogram averaged consensus structure of the malarial 80S ribo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tpu
TitleSubtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 39
  • (Large ribosomal subunit protein ...) x 2
  • (Ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Receptor for activated c kinase
  • Small ribosomal subunit protein eS30
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / malaria / cryoET / in situ / Plasmodium falciparum / 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 / 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) / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / 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) / protein-RNA complex assembly / translation regulator activity / 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) / 90S preribosome / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / large ribosomal subunit / ribosome binding / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / ubiquitin-dependent protein catabolic process / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
: / 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 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 S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L10e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S19A/S15e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / 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 S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 60S ribosomal protein L19 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / 60S ribosomal protein L35 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 / 60S ribosomal protein L6, putative / 40S ribosomal protein S11 / 60S ribosomal protein L39 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 / 60S ribosomal protein L6, putative / 40S ribosomal protein S11 / 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 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS30 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS12 / 60S ribosomal protein L7, putative / Small ribosomal subunit protein eS1 / 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 / Receptor for activated c kinase / 40S ribosomal protein S5, putative / 40S ribosomal protein S10, putative / 60S ribosomal protein L11a, putative / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S15 / 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 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 L13, putative / 40S ribosomal protein S20e, putative / 40S ribosomal protein S3 / 60S ribosomal protein L27 / 40S ribosomal protein S5 / 60S ribosomal protein L14, putative / 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 speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.1 Å
AuthorsAnton, L. / Cheng, W. / Zhu, X. / Ho, C.M.
Funding support United States, Switzerland, France, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD029613 United States
Swiss National Science Foundation Switzerland
Human Frontier Science Program (HFSP) France
CitationJournal: To Be Published
Title: Divergent translational landscape reflects adaptation to biased codon usage in malaria parasites
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
DepositionAug 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S1: 40S ribosomal protein S24
S2: 40S ribosomal protein S25
S3: 40S ribosomal protein S26
S4: 40S ribosomal protein S27
S5: 60S ribosomal protein L41
S6: Small ribosomal subunit protein eS30
S7: 60S ribosomal protein L24, putative
SA: 18S ribosomal RNA
SB: 40S ribosomal protein S3a
SC: 40S ribosomal protein SA
SD: 40S ribosomal protein S3
SE: 40S ribosomal protein S9, putative
SF: 40S ribosomal protein S4
SG: 40S ribosomal protein S5
SH: 40S ribosomal protein S6
SI: 40S ribosomal protein S5, putative
SJ: 40S ribosomal protein S7
SK: 40S ribosomal protein S15A, putative
SL: 40S ribosomal protein S8
SM: 40S ribosomal protein S16
SN: 40S ribosomal protein S20e, putative
SO: 40S ribosomal protein S10, putative
SP: 40S ribosomal protein S11
SQ: 40S ribosomal protein S23, putative
SR: 40S ribosomal protein S12
SS: 40S ribosomal protein S18, putative
ST: 40S ribosomal protein S29, putative
SU: 40S ribosomal protein S15
SV: 40S ribosomal protein S11, putative
SW: 40S ribosomal protein S17, putative
SX: 40S ribosomal protein S19
SY: 40S ribosomal protein S19
SZ: 40S ribosomal protein S21
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, putative
A7: 60S ribosomal protein L31
AN: 60S ribosomal protein L14, putative
A8: 60S ribosomal protein L32
A9: 60S ribosomal protein L35ae, putative
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, putative
AJ: 60S ribosomal protein L7a
Ac: Ribosomal protein L37
AK: 60S ribosomal protein L13, putative
AM: 60S ribosomal protein L23, putative
AS: 60S ribosomal protein L18-2, putative
AO: 60S ribosomal protein L27a, putative
AQ: 60S ribosomal protein L10, putative
AR: 60S ribosomal protein L5, putative
AW: 60S ribosomal protein L17, putative
AY: 60S ribosomal protein L23
AT: 60S ribosomal protein L19
AZ: 60S ribosomal protein L26, putative
A3: 60S ribosomal protein L35, putative
A5: 60S ribosomal protein L7, putative
AD: 60S ribosomal protein L2
AE: 60S ribosomal protein L3
AF: 60S ribosomal protein L4
AG: 60S ribosomal protein L11a, putative
AU: 60S ribosomal protein L18a
AH: 60S ribosomal protein L6, putative
AV: 60S ribosomal protein L21
Ag: 60S ribosomal protein L41
AX: 60S ribosomal protein L22, putative
A0: 60S ribosomal protein L24, putative
S8: Receptor for activated c kinase


Theoretical massNumber of molelcules
Total (without water)3,419,26579
Polymers3,419,26579
Non-polymers00
Water00
1


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

-
Components

+
40S ribosomal protein ... , 29 types, 29 molecules S1S2S3S4SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ

#1: 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
#2: 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
#3: 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
#4: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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

+
60S ribosomal protein ... , 39 types, 39 molecules S5S7ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5AD...

#5: Protein 60S ribosomal protein L41


Mass: 6516.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#7: RNA chain 60S ribosomal protein L24, putative


Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#37: 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
#38: 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
#39: Protein 60S ribosomal protein L28


Mass: 14309.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#40: 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
#41: Protein 60S ribosomal protein L30e, putative


Mass: 11679.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#42: 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
#43: 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
#44: Protein 60S ribosomal protein L32


Mass: 15466.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#45: Protein 60S ribosomal protein L35ae, putative


Mass: 16249.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#46: Protein 60S ribosomal protein L34


Mass: 17349.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#47: 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
#48: 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
#49: 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
#54: 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
#55: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: Protein 60S ribosomal protein L17, putative


Mass: 19431.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#75: Protein 60S ribosomal protein L21


Mass: 18969.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#76: 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
#77: Protein 60S ribosomal protein L22, putative


Mass: 16422.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IB51
#78: 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

-
Protein/peptide , 1 types, 1 molecules S6

#6: Protein/peptide Small ribosomal subunit protein eS30


Mass: 4925.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96269

-
RNA chain , 4 types, 4 molecules SAAAACAB

#8: RNA chain 18S ribosomal RNA


Mass: 669744.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1013064538
#34: RNA chain 28S ribosomal RNA


Mass: 1216212.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#35: 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
#36: 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)

-
Protein , 2 types, 2 molecules AfS8

#50: 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
#79: Protein Receptor for activated c kinase


Mass: 35726.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBA0

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

#51: Protein Ribosomal protein L15


Mass: 23985.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#56: 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

#52: Protein Large ribosomal subunit protein eL43


Mass: 10755.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#53: Protein Large ribosomal subunit protein eL42


Mass: 12065.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Plasmodium falciparum 80S ribosome consensus structure
Type: RIBOSOME
Details: Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Entity ID: #1-#4, #51-#75, #5-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 2800 nm
Image recordingElectron dose: 2.93 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 500.24002 Å / B: 500.24002 Å / C: 500.24002 Å / Space group name: C1 / Space group num: 1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120226 / Symmetry type: 3D CRYSTAL
EM volume selectionNum. of tomograms: 848 / Num. of volumes extracted: 129617
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 136.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0031209936
ELECTRON MICROSCOPYf_angle_d0.6118307619
ELECTRON MICROSCOPYf_chiral_restr0.035738550
ELECTRON MICROSCOPYf_plane_restr0.004419791
ELECTRON MICROSCOPYf_dihedral_angle_d16.546173375

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more