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- PDB-6okk: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Entry
Database: PDB / ID: 6okk
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
  • E-site tRNA
Keywordsribosome/inhibitor / Protein synthesis / antimalarial drug / RIBOSOME / ribosome-inhibitor complex
Function / homology
Function and homology information


RMTs methylate histone arginines / Protein methylation / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...RMTs methylate histone arginines / Protein methylation / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 ...Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / : / Ribosomal protein S12e / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S26e / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Double Stranded RNA Binding Domain / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e
Similarity search - Domain/homology
emetine / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 / 40S ribosomal protein S29, putative / 40S ribosomal protein S19 / 40S ribosomal protein S11, putative / 40S ribosomal protein S15A, putative ...emetine / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S16 / 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 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 / 40S ribosomal protein S20e, putative / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / 40S ribosomal protein S5 / 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: 3.3 Å
AuthorsWong, W. / Scheres, S.H.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1053801, APP1024678 Australia
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
DepositionApr 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 18S ribosomal RNA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein SA
D: 40S ribosomal protein S3
E: 40S ribosomal protein S9
F: 40S ribosomal protein S4
G: 40S ribosomal protein S5
H: 40S ribosomal protein S6
I: 40S ribosomal protein S5
J: 40S ribosomal protein S7
K: 40S ribosomal protein S15A
L: 40S ribosomal protein S8
M: 40S ribosomal protein S16
N: 40S ribosomal protein S20e
O: 40S ribosomal protein S10
P: 40S ribosomal protein S11
Q: 40S ribosomal protein S23
R: 40S ribosomal protein S12
S: 40S ribosomal protein S18
T: 40S ribosomal protein S29
U: 40S ribosomal protein S15
V: 40S ribosomal protein S11
W: 40S ribosomal protein S17
X: 40S ribosomal protein S19
Y: 40S ribosomal protein S19
Z: 40S ribosomal protein S21
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28e
f: 40S ribosomal protein S30
g: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,060102
Polymers1,260,88533
Non-polymers2,17469
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules Ag

#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 (isolate 3D7) (eukaryote)
Strain: isolate 3D7
#33: RNA chain E-site tRNA


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

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

#2: Protein 40S ribosomal protein S3a /


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


Mass: 29891.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IJD4
#4: Protein 40S ribosomal protein S3 /


Mass: 24709.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IKH8
#5: Protein 40S ribosomal protein S9 /


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


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


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


Mass: 35473.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IDR9
#9: Protein 40S ribosomal protein S5 /


Mass: 21898.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IBN5
#10: Protein 40S ribosomal protein S7 /


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


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


Mass: 25105.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IM10
#13: Protein 40S ribosomal protein S16 /


Mass: 16318.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: A0A0L7M7C8
#14: Protein 40S ribosomal protein S20e / Ribosome


Mass: 13534.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IK02
#15: Protein 40S ribosomal protein S10 /


Mass: 16510.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IBQ5
#16: Protein 40S ribosomal protein S11 /


Mass: 16105.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I3U6
#17: Protein 40S ribosomal protein S23 /


Mass: 16166.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O97248
#18: Protein 40S ribosomal protein S12 /


Mass: 15414.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O97249
#19: Protein 40S ribosomal protein S18 /


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


Mass: 6430.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: C0H4K8
#21: Protein 40S ribosomal protein S15 /


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


Mass: 18801.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O77381
#23: Protein 40S ribosomal protein S17 /


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


Mass: 16800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: C0H5C2
#25: Protein 40S ribosomal protein S19 /


Mass: 19757.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IFP2
#26: Protein 40S ribosomal protein S21 /


Mass: 9157.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IHS5
#27: Protein 40S ribosomal protein S24 /


Mass: 15431.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I3R6
#28: Protein 40S ribosomal protein S25 /


Mass: 11691.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8ILN8
#29: Protein 40S ribosomal protein S26 /


Mass: 12539.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O96258
#30: Protein 40S ribosomal protein S27 /


Mass: 9154.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IEN2
#31: Protein 40S ribosomal protein S28e / Ribosome


Mass: 7508.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IKL9
#32: Protein 40S ribosomal protein S30 /


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


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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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, small subunit
Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL
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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4RELIONCTF correction
7UCSF Chimeramodel fitting
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105247 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å

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