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- PDB-3j7a: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Basic information

Entry
Database: PDB / ID: 3j7a
TitleCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • tRNA
KeywordsRIBOSOME/INHIBITOR / emetine / RIBOSOME-INHIBITOR complex
Function / homology
Function and homology information


RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / 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 ...RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / 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) / Ub-specific processing proteases / 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) / 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 / mRNA 5'-UTR binding / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S4, central domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / Ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S4, central domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 / Diphtheria Toxin Repressor; domain 2 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / N-terminal domain of TfIIb / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Single Sheet / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S28e conserved site
Similarity search - Domain/homology
emetine / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S29, putative / 40S ribosomal protein S19 / 40S ribosomal protein S11, putative / 40S ribosomal protein S15A, putative / 40S ribosomal protein S26 ...emetine / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S29, putative / 40S ribosomal protein S19 / 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 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S9, putative / 40S ribosomal protein S24 / 40S ribosomal protein S11 / 40S ribosomal protein S17, putative / 40S ribosomal protein S16, putative / 40S ribosomal protein S5, putative / 40S ribosomal protein S10, putative / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 40S ribosomal protein S18, putative / 40S ribosomal protein S4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / Small ribosomal subunit protein uS5 / 40S ribosomal protein S25 / 40S ribosomal protein S8
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWong, W. / Bai, X.C. / Brown, A. / Fernandez, I.S. / Hanssen, E. / Condron, M. / Tan, Y.H. / Baum, J. / Scheres, S.H.W.
CitationJournal: Elife / Year: 2014
Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Authors: Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres /
Abstract: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Structure summary
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: 18S ribosomal RNA
B: 40S ribosomal protein eS1
C: 40S ribosomal protein uS2
D: 40S ribosomal protein uS3
E: 40S ribosomal protein uS4
F: 40S ribosomal protein eS4
G: 40S ribosomal protein uS5
H: 40S ribosomal protein eS6
I: 40S ribosomal protein uS7
J: 40S ribosomal protein eS7
K: 40S ribosomal protein uS8
L: 40S ribosomal protein eS8
M: 40S ribosomal protein uS9
N: 40S ribosomal protein uS10
O: 40S ribosomal protein eS10
P: 40S ribosomal protein uS11
Q: 40S ribosomal protein uS12
R: 40S ribosomal protein eS12
S: 40S ribosomal protein uS13
T: 40S ribosomal protein uS14
U: 40S ribosomal protein uS15
V: 40S ribosomal protein uS17
W: 40S ribosomal protein eS17
X: 40S ribosomal protein uS19
Y: 40S ribosomal protein eS19
Z: 40S ribosomal protein eS21
1: 40S ribosomal protein eS24
2: 40S ribosomal protein eS25
3: 40S ribosomal protein eS26
4: 40S ribosomal protein eS27
5: 40S ribosomal protein eS28
6: 40S ribosomal protein eS30
7: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,060102
Polymers1,260,88533
Non-polymers2,17469
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules A7

#1: RNA chain 18S ribosomal RNA


Mass: 671337.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7
#33: RNA chain tRNA


Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7

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40S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ123456

#2: Protein 40S ribosomal protein eS1


Mass: 30111.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97313
#3: Protein 40S ribosomal protein uS2


Mass: 29891.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IJD4
#4: Protein 40S ribosomal protein uS3


Mass: 24709.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IKH8
#5: Protein 40S ribosomal protein uS4


Mass: 22172.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3R0
#6: Protein 40S ribosomal protein eS4


Mass: 29830.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IIU8
#7: Protein 40S ribosomal protein uS5


Mass: 30008.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IL02
#8: Protein 40S ribosomal protein eS6


Mass: 35473.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDR9
#9: Protein 40S ribosomal protein uS7


Mass: 21898.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBN5
#10: Protein 40S ribosomal protein eS7


Mass: 22524.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IET7
#11: Protein 40S ribosomal protein uS8


Mass: 14900.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O77395
#12: Protein 40S ribosomal protein eS8


Mass: 25105.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IM10
#13: Protein 40S ribosomal protein uS9


Mass: 16318.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IAX5
#14: Protein 40S ribosomal protein uS10


Mass: 13534.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IK02
#15: Protein 40S ribosomal protein eS10


Mass: 16510.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBQ5
#16: Protein 40S ribosomal protein uS11


Mass: 16105.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3U6
#17: Protein 40S ribosomal protein uS12


Mass: 16166.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97248
#18: Protein 40S ribosomal protein eS12


Mass: 15414.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97249
#19: Protein 40S ribosomal protein uS13


Mass: 17928.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IIA2
#20: Protein 40S ribosomal protein uS14


Mass: 6430.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H4K8
#21: Protein 40S ribosomal protein uS15


Mass: 17286.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDB0
#22: Protein 40S ribosomal protein uS17


Mass: 18801.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O77381
#23: Protein 40S ribosomal protein eS17


Mass: 16096.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I502
#24: Protein 40S ribosomal protein uS19


Mass: 16800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H5C2
#25: Protein 40S ribosomal protein eS19


Mass: 19757.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IFP2
#26: Protein 40S ribosomal protein eS21


Mass: 9157.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IHS5
#27: Protein 40S ribosomal protein eS24


Mass: 15431.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3R6
#28: Protein 40S ribosomal protein eS25


Mass: 11691.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILN8
#29: Protein 40S ribosomal protein eS26


Mass: 12539.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O96258
#30: Protein 40S ribosomal protein eS27


Mass: 9154.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IEN2
#31: Protein 40S ribosomal protein eS28


Mass: 7508.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IKL9
#32: Protein 40S ribosomal protein eS30


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

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Non-polymers , 3 types, 69 molecules

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


Mass: 24.305 Da / Num. of mol.: 67 / Source method: obtained synthetically / Formula: Mg
#35: Chemical ChemComp-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan


Mass: 480.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O4
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Type: RIBOSOME
Molecular weightValue: 4.2 MDa / Experimental value: NO
Buffer solutionName: 20 mM HEPES, pH 7.4, 40 mM potassium acetate, 10 mM ammonium acetate, 10 mM magnesium acetate, 5 mM BME
pH: 7.4
Details: 20 mM HEPES, pH 7.4, 40 mM potassium acetate, 10 mM ammonium acetate, 10 mM magnesium acetate, 5 mM BME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon grids (Quantifoil R2/2) with home-made continuous carbon film, glow-discharged 30 seconds
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 %
Details: Blot 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jan 19, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 X / Calibrated magnification: 104748 X / Nominal defocus max: 3800 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN / Temperature: 85 K / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Details: An in-house system was used to intercept videos from the detector at a rate of 17 frames/second (1 second exposures).
Image scansNum. digital images: 1083
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0077 2014/05/16 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105247 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å
Details: A newly developed statistical movie processing approach was used to compensate for beam-induced movement.
Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms32915 35848 103 0 68866

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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

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