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- EMDB-8576: Structure of the Plasmodium falciparum 80S ribosome bound to the ... -

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Basic information

Entry
Database: EMDB / ID: 8576
TitleStructure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine
Map data
SamplePlasmodium falciparum 80S ribosome bound to mefloquine:
(nucleic-acidNucleic acid) x 3 / (60S ribosomal protein ...) x 39 / (Ribosomal protein ...) x 2 / Ubiquitin-60S ribosomal protein L40 / (ligand) x 3
Function / homologyRibosomal protein L7A/L8 superfamily / Ribosomal protein L23 / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e ...Ribosomal protein L7A/L8 superfamily / Ribosomal protein L23 / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L5 / Ribosomal protein L38e superfamily / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L29 protein / Ribosomal protein L22e superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L44 / Ribosomal protein L5, N-terminal / Ribosomal protein L39e domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L21 superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal L39 protein / Ribosomal L40e family / MAPK6/MAPK4 signaling / Ribosomal protein L37e signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ubiquitin domain signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L13e signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L18e signature. / Ribosomal protein L31e signature. / Ribosomal protein L34e signature. / Ribosomal protein L21e signature. / Ribosomal protein L44e signature. / Ribosomal protein L36e signature. / Ribosomal protein L15e signature. / Ribosomal protein L10e signature. / Ubiquitin domain profile. / Translesion Synthesis by POLH / L13a-mediated translational silencing of Ceruloplasmin expression / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L21e / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e / Ribosomal protein L6e / Ribosomal protein L31e / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal L22e protein family / Ribosomal L18 C-terminal region / Ribosomal L27e protein family / Ribosomal L28e protein family / Ribosomal L29e protein family / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e
Function and homology information
SourcePlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsWong W / Bai X-C
CitationJournal: Nat Microbiol / Year: 2017
Title: Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.
Authors: Wilson Wong / Xiao-Chen Bai / Brad E Sleebs / Tony Triglia / Alan Brown / Jennifer K Thompson / Katherine E Jackson / Eric Hanssen / Danushka S Marapana / Israel S Fernandez / Stuart A Ralph / Alan F Cowman / Sjors H W Scheres / Jake Baum
Abstract: Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, ...Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-generation derivatives to improve drug potency towards inhibition of their molecular targets. Mefloquine is a widely used antimalarial without a known mode of action. Here, we demonstrate that mefloquine is a protein synthesis inhibitor. We solved a 3.2 Å cryo-electron microscopy structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre. Mutagenesis of mefloquine-binding residues generates parasites with increased resistance, confirming the parasite-killing mechanism. Furthermore, structure-guided derivatives with an altered piperidine group, predicted to improve binding, show enhanced parasiticidal effect. These data reveal one possible mode of action for mefloquine and demonstrate the vast potential of cryo-electron microscopy to guide the development of mefloquine derivatives to inhibit parasite protein synthesis.
Validation ReportPDB-ID: 5umd

SummaryFull reportAbout validation report
DateDeposition: Jan 27, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5umd
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8576.map.gz (map file in CCP4 format, 364501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
450 pix
1.03 Å/pix.
= 463.5 Å
450 pix
1.03 Å/pix.
= 463.5 Å
450 pix
1.03 Å/pix.
= 463.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.5065006 - 0.8825569
Average (Standard dev.)0.0001856431 (0.033729594)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions450450450
Origin000
Limit449449449
Spacing450450450
CellA=B=C: 603 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z463.500463.500463.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.5070.8830.000

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Supplemental data

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Sample components

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Entire Plasmodium falciparum 80S ribosome bound to mefloquine

EntireName: Plasmodium falciparum 80S ribosome bound to mefloquine
Number of components: 49
MassTheoretical: 4.2 MDa

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Component #1: protein, Plasmodium falciparum 80S ribosome bound to mefloquine

ProteinName: Plasmodium falciparum 80S ribosome bound to mefloquine
Recombinant expression: No
MassTheoretical: 4.2 MDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)
Source (natural)Location in cell: cytoplasm

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Component #2: nucleic-acid, 28S ribosomal RNA

Nucleic-acidName: 28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUGAUUUG AUGUUAGGAG GGCAAAUCCG CCGAAUUUAA GCAUAUAAUU AAGCGGAAGA AAAGAAAAUA ACUAUGAUUC CUUUAGUAAC GGCGAGUGAA CAAGGACCAG CUCAAACGGU UAAUCCUUCG UUUGGUGCAA ACCUUUCGAC GGAAUUGUCG UUGAAUUAUU CCAUGAAUGC CUUUAAUUUG AGCAAAGUGA GCAGGAAUGC UUCCCCAUAG AGGGUGAAAG GCCCAUAGUU CUUUUUAAUU UAUUCAUUGG AAUUUUUCAU GUCGAGUCGU GUUCUUUGAG AUUGGAGCAC UAAUACGUGU GAUACAUUUC ACAUAAAGCU AAAUAUAUGU AGGAGACCGA UAGCAAACAA GUACCGUGAG GGAAAGAUGA AAUAGUACUC AGGAAUGAGC AAUUAAAUAG UACCUGAAAU CGUUAAGAUG GAACGGAUUA AGAGAGAAAA CAAGUAAAGA GGGGAAUUUU UAAUUUUUUU UGUUAUAAUU CUCUUCUUUA UUAAAAGAAA CAUCAGUGAU UAAUUUAAUU UCAAUAAAGC AAUCCCCUGA AAUUCAAAAU UUCUUUUAAU UUUGUUUUCA CUUUCUCCCC GCACUAAUGU GGGGAAAACU GGCUUUAUUU CUUCAAUUAU UUUUUUUGCU GAGGAAUUUU AAAAUUAUUU GAAUUUUUCU UCUUAUAAUU UAAGUUGUUU CUAUACAGUA CUUUCUUAAC CCACUCGUCU UGAAACACGG ACCAAGGAGU CUAGCAAAUG UGCAAGUGUA UAUGAUUCUU UAAACAUUUC UCUUUUUAAU AUACGCAUAA UUAAUGUAAU AUGUUUUCUU CAUUGUAGAU UUGUGGUGUU UAAUUUUUAU UAAAUCCCCA CUUUGCAUAC AAUACCGGUA AGCAAUUAUG CUUUAUUGAG UACGAGCAUA UUUGGUAGGA CCCGAGAGGC UUUGAACUAA GCGUGAUGAG AUUGAAGUCA GACGAAAGUC UGAUGGAGGA UCGAGUUGAU ACUGACGUGC AAAUCGUUCA UUUCAAUCAC GUUUAGGGGC GAAAGACUAA UCGAAAAGCC UAUUAGCUGG UUAUUUUCGA AAGAUCUCUC AGGAUCGCUG GAGUUGAUUA AUAUAAUUUU ACCAGGUAGA GAUAAUGAUU AGAGGAAUCA GGGAAAUCGU UUUCCUUGAC CUAUUCUCAA ACUCCCAAUA GGUAAAAAGG GCGAAAUAAC UCAAUUUGUA UUUCACUCAU AUUAAAUAAA AUAACUCCAA GUGGGCCAUU UUUGGUAAGC AGAACUGGCG AUGAGGGAUG CUCCUAACGC UUGGAUAAGG UGCCUAAAUA UUCGCUCAUG AGAUCCCAUA AAAGGUGUUG GUUCAUAAUG ACAGUAGGAC GGUGGUCAUG GAAGUCGAAA UCCGCUAAGG AGUGUGUAAC AACUCACCUA CCGAAUGAAC UAGCCCUGAA AAUGGAUGGC GCUAAAGCGG AUUACCGAUA CCAAGCCAUA AAAAGAACAG AAAAAAUUUA UUUUUUUUUU AGAAUCUUUU UAUGAGUAGA AAAUCGUGGG GUUUGUGUUG AAGCGAAAUA CGUGAGUUUU CGUGGAACAU CUCCCUAGUG CAGAUCUUGG UGGAAGUAGC AACUAUUCAA AUGAGAACUU UGAAGACUGA AGUGGAGAAG GGUUUCUUGU CAACUGUGAU UGAACAAGAG UUAGCCGCUC CUAAGGGAUA GCUGAAAAGU GUUUAAAAGG GGGUUCCUUC CCCGUCUCAA AAGGGAAACA GGUUGAUAUU CCUGUGCCAA UAGUAUUAUG AGUUUCUUAG AUGGUAACAU AUAUAUAAAU GAACUCCUUU ACAUAGGCUU UACACUCGGG GUGCGUUUUC UUUGCACUUU ACCUUUAUAA CAAACCUUGG AAUCAAUUUA CUUGGAGAAG AGGUUCGUUG AACUCAAUUC AAAAAAUUUC UUGAACGGGG UUUUCGGAUU CAGUUCAUUU UAUUUUUUGU UUUGUAGCAA UAGUAAUUCG UUUUUAUGAA UUAUCCGAAG UGGUAAGGAC UAUCCUUGAA AAAAGGAGGG AACGGCUUUG UAACUUGGUU UCUUCUGAUU CCAUUUUGCU UUGCUUAUAC UCUUAAUACU UGUAUGAGCG UACCAACAAC CGCAUCAGGU CUCCAAGGUU AACAGCCUCU GGUUAAAUAG AAAAAAGUAG GUAAGGGAAG UCGGCAAAAU AGAUCCGUAA CUUCGGGAAA AGGAUUGGCU CUGAGGACAU UAGAAAAGAG AAGAAAAAAA GAGGGUCGAA AAUAAAAUUG CAGUCUUUAU UUGCUUUUCU UUCGAUUUGC UUGUAAUCUG CUUUUUCUUU UUCUUCUUUC UUUUUUUCUC CCCCUCUUUU CGCCUUCACU UUAUUGUAAU UUUAUUACUU UAAUUUGAUA CCUAUAAUGU UAACUCAGAA CUGAAACGGA CAAGGGGAAU CCGACUGUUU AAUUAAAACA UAGCAUUGUG AAAAGCCACA ACUGGUAUUA ACACAAUGUG AUUUCUGCCC AGUGCUUUGA AUGUCAACUU GAUGAAAUUC AAUCAAGCGC AGGUAAACGG CGGGAGUAAC UAUGACUCUC UUAAGGUAGC CAAAUGCCUC GUCAUCUAAU UAGUGACGCG CAUGAAUGGA UUAACGAGAU UCCCACUGUC CCUACUUGCU AUCUAGCGAA ACCACAGCCA AGGGAACGGG CUUGGCAAAA UCAGCGGGGA AAGAAGACCC UGUUGAGCUU UACUCUAGUC UGGCUUUGUG AAACGACUUA AGAGGUGUAG CAUAAGUGGG AGUAGAAACU GAAAUAUGUU UUUACGACAG UGAAAUACCA CUACUUUUAA AGUUGUUUUA CUUAUCCAUU UAUAGGGAAA UAUAUUAUGC UUUAUCCUUC GGGAAGGCAU UCUGAUAUUA UUUGAAUUUU UAAGAAACUU GUUUCUUAUC UUUCUCCCAA UUUCUAUGGA GACAUAGCCA GGUGGGGAGU UUGACUGGGG CGGUACAUCU GUUAAAUAUU AACGCAGAUG UCCAAAGACA AGCUCAAAGA GAACAGAAAU CUCUUGUAGA CUAAAAGGGG AAAAGCUUGU UUGAUUUCUA UUUUCAGAAC AAGUAGAAAA CGUGAAAGCG UGGCCUAUCG AUCCUUUAUA UUUGCAAAAU GACGUAAAUU ACUUACUACU GUGCAUAUAG AGGUGUCUGA AAAGUUACCA CAGGGAUAAC UGGCUUGUGG CUGCCAAGCG CUCCUAGCGA CGUAGCUUUU UGAUCCUUCG AUGUCGGCUC UUCCUAUCAU UGGGACGCAG AAGUCUCAAA GUGUCGGAUU GUUCACCCGC UAAUAGGGAA CGUGAGCUGG GUUUAGACCG UCGUGAGACA GGUUAGUUUU ACCCUACUGA UGAAUUUUAU UAUAUUUUUU AUAUAUACAU AUAGUAUUGU GACAGUAAUC CAACUUGGUA CGAGAGGAUU AGUUGGUUCA GACAAUUGGU ACAGCAAUUG GUUGACAAAC CAGUGUUGCG AAGCUAAGUC UGUUGGAUAA UGGCUGAACG CCUCUUAAGC CAGAAACCAU GCUGAUUAAA CAAUACUAUU UCGUUCUUUU UUGUUUCCUU UUUUACUGCU AAUGUAAAAG AGAAAUUAUA UAUGUACCUU UUUUUGGUAC AUAAAUAAUC CUAUCACCUU UUUCGUGAGC UGUGAGCUGU GAGCUAGGCA AUAGUUCUUU AACAACAAAA AAGAAUUGCA CAAACUGUAG ACGACUUUUU UGCCUCAGGG UGCUGUAAAC AUGAAAGUAA ACUUUGUUUU ACGAUCUGUU GAGGCUUAUC CCUAGUGGUA AAGUGUUU
MassTheoretical: 1.216212125 MDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #3: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGACUCGUUC AUACUACAGU GGAUACACCA GAUCCCAUCA GAACUCUGAA GUUAAGCACU GUAAGGCUUG GCUAGUACUG AGGUGGGAGA CCGCUCGGGA ACACCAGGUG AUGAGUCAG
MassTheoretical: 38.410859 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #4: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAGCACAGUC UUAACGAUGG AUGUCUUGGU UCCUACAGCG AUGAAGGCCG CAGCAAAAUG CGAUACGCAA UGAAAAUUGC AGUGACUGUG AAUCAUCAGA AUGCUGAAUG UAAACUACAC CAAUUCCCUU CGGGGAAUAG UGGUACUCCU ACAGAAAAU
MassTheoretical: 51.206461 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #5: protein, 60S ribosomal protein L2

ProteinName: 60S ribosomal protein L2 / Recombinant expression: No
MassTheoretical: 28.064998 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #6: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 44.31818 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #7: protein, 60S ribosomal protein L4

ProteinName: 60S ribosomal protein L4 / Recombinant expression: No
MassTheoretical: 46.311688 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #8: protein, 60S ribosomal protein L11a, putative

ProteinName: 60S ribosomal protein L11a, putative / Recombinant expression: No
MassTheoretical: 20.268666 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #9: protein, 60S ribosomal protein L6, putative

ProteinName: 60S ribosomal protein L6, putative / Recombinant expression: No
MassTheoretical: 21.638562 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #10: protein, 60S ribosomal protein L6-2, putative

ProteinName: 60S ribosomal protein L6-2, putative / Recombinant expression: No
MassTheoretical: 25.587623 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #11: protein, 60S ribosomal protein L7-3, putative

ProteinName: 60S ribosomal protein L7-3, putative / Recombinant expression: No
MassTheoretical: 32.760455 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #12: protein, 60S ribosomal protein L13, putative

ProteinName: 60S ribosomal protein L13, putative / Recombinant expression: No
MassTheoretical: 23.805344 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #13: protein, 60S ribosomal protein L13

ProteinName: 60S ribosomal protein L13 / Recombinant expression: No
MassTheoretical: 25.454143 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #14: protein, 60S ribosomal protein L23, putative

ProteinName: 60S ribosomal protein L23, putative / Recombinant expression: No
MassTheoretical: 15.015713 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #15: protein, 60S ribosomal protein L14, putative

ProteinName: 60S ribosomal protein L14, putative / Recombinant expression: No
MassTheoretical: 19.340373 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #16: protein, 60S ribosomal protein L27a, putative

ProteinName: 60S ribosomal protein L27a, putative / Recombinant expression: No
MassTheoretical: 16.765834 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #17: protein, Ribosomal protein L15

ProteinName: Ribosomal protein L15Ribosome / Recombinant expression: No
MassTheoretical: 24.19766 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #18: protein, 60S ribosomal protein L10, putative

ProteinName: 60S ribosomal protein L10, putative / Recombinant expression: No
MassTheoretical: 25.26548 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #19: protein, 60S ribosomal protein L5, putative

ProteinName: 60S ribosomal protein L5, putative / Recombinant expression: No
MassTheoretical: 34.067352 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #20: protein, 60S ribosomal protein L18-2, putative

ProteinName: 60S ribosomal protein L18-2, putative / Recombinant expression: No
MassTheoretical: 21.508783 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #21: protein, 60S ribosomal protein L19

ProteinName: 60S ribosomal protein L19 / Recombinant expression: No
MassTheoretical: 21.641096 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #22: protein, 60S ribosomal protein L18a

ProteinName: 60S ribosomal protein L18a / Recombinant expression: No
MassTheoretical: 21.793611 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #23: protein, 60S ribosomal protein L21

ProteinName: 60S ribosomal protein L21 / Recombinant expression: No
MassTheoretical: 18.840244 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #24: protein, 60S ribosomal protein L17, putative

ProteinName: 60S ribosomal protein L17, putative / Recombinant expression: No
MassTheoretical: 23.469926 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #25: protein, 60S ribosomal protein L22, putative

ProteinName: 60S ribosomal protein L22, putative / Recombinant expression: No
MassTheoretical: 16.42293 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #26: protein, 60S ribosomal protein L23

ProteinName: 60S ribosomal protein L23 / Recombinant expression: No
MassTheoretical: 22.152748 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #27: protein, 60S ribosomal protein L26, putative

ProteinName: 60S ribosomal protein L26, putative / Recombinant expression: No
MassTheoretical: 14.855709 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #28: protein, 60S ribosomal protein L24, putative

ProteinName: 60S ribosomal protein L24, putative / Recombinant expression: No
MassTheoretical: 19.29593 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #29: protein, 60S ribosomal protein L27

ProteinName: 60S ribosomal protein L27 / Recombinant expression: No
MassTheoretical: 16.78518 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #30: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 14.437823 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #31: protein, 60S ribosomal protein L35, putative

ProteinName: 60S ribosomal protein L35, putative / Recombinant expression: No
MassTheoretical: 14.787824 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #32: protein, 60S ribosomal protein L29, putative

ProteinName: 60S ribosomal protein L29, putative / Recombinant expression: No
MassTheoretical: 8.041588 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #33: protein, 60S ribosomal protein L7, putative

ProteinName: 60S ribosomal protein L7, putative / Recombinant expression: No
MassTheoretical: 30.593184 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #34: protein, 60S ribosomal protein L30e, putative

ProteinName: 60S ribosomal protein L30e, putative / Recombinant expression: No
MassTheoretical: 11.79476 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #35: protein, 60S ribosomal protein L31

ProteinName: 60S ribosomal protein L31 / Recombinant expression: No
MassTheoretical: 14.099854 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #36: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 15.565751 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #37: protein, 60S ribosomal protein L35Ae, putative

ProteinName: 60S ribosomal protein L35Ae, putative / Recombinant expression: No
MassTheoretical: 16.306425 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #38: protein, 60S ribosomal protein L34

ProteinName: 60S ribosomal protein L34 / Recombinant expression: No
MassTheoretical: 17.406967 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #39: protein, 60S ribosomal protein L36

ProteinName: 60S ribosomal protein L36 / Recombinant expression: No
MassTheoretical: 12.82544 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #40: protein, Ribosomal protein L37

ProteinName: Ribosomal protein L37Ribosome / Recombinant expression: No
MassTheoretical: 10.571592 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #41: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Recombinant expression: No
MassTheoretical: 10.341729 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #42: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Recombinant expression: No
MassTheoretical: 6.540912 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #43: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Recombinant expression: No
MassTheoretical: 14.645169 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #44: protein, 60S ribosomal protein L41

ProteinName: 60S ribosomal protein L41 / Recombinant expression: No
MassTheoretical: 5.10831 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #45: protein, 60S ribosomal protein L37a

ProteinName: 60S ribosomal protein L37a / Recombinant expression: No
MassTheoretical: 10.826083 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #46: protein, 60S ribosomal protein L44

ProteinName: 60S ribosomal protein L44 / Recombinant expression: No
MassTheoretical: 12.194902 kDa
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #47: ligand, Mefloquine

LigandName: Mefloquine / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.378312 kDa

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Component #48: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 164 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #49: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Hepes pH 7.4, 40 mM KAc, 10 mM NH4Ac, 10 mM Mg(Ac)2 and 5 mM 2-mecaptoethanol
pH: 7.4
Support filmBlot 2.5s before plunging
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000 X (nominal), 104748 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 80 - 90 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43184
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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About Yorodumi

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News

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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

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Related info.: Omokage search

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EM Navigator & Yorodumi renewed

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Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

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Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

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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