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- PDB-5umd: Structure of the Plasmodium falciparum 80S ribosome bound to the ... -

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Entry
Database: PDB / ID: 5umd
TitleStructure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine
DescriptorUbiquitin-60S ribosomal protein L40
(60S ribosomal protein ...) x 39
(ribosomal protein ...) x 2
KeywordsRIBOSOME / Ribosome / protein synthesis / antimalarial
Specimen sourcePlasmodium falciparum 3d7 / eukaryote / image: Plasmodium falciparum
MethodElectron microscopy (3.2 A resolution / Single particle)
AuthorsWong, W. / Bai, X.-C. / Brown, A. / Scheres, S. / Baum, J.
CitationNat Microbiol, 2017, 2, 17031-17031

Nat Microbiol, 2017, 2, 17031-17031 StrPapers
Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.
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

DateDeposition: Jan 27, 2017 / Release: Mar 1, 2017 / Last modification: Mar 22, 2017

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Assembly

Deposited unit
A: 28S ribosomal RNA
B: 5S ribosomal RNA
C: 5.8S ribosomal RNA
D: 60S ribosomal protein L2
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4
G: 60S ribosomal protein L11a, putative
H: 60S ribosomal protein L6, putative
I: 60S ribosomal protein L6-2, putative
J: 60S ribosomal protein L7-3, putative
K: 60S ribosomal protein L13, putative
L: 60S ribosomal protein L13
M: 60S ribosomal protein L23, putative
N: 60S ribosomal protein L14, putative
O: 60S ribosomal protein L27a, putative
P: Ribosomal protein L15
Q: 60S ribosomal protein L10, putative
R: 60S ribosomal protein L5, putative
S: 60S ribosomal protein L18-2, putative
T: 60S ribosomal protein L19
U: 60S ribosomal protein L18a
V: 60S ribosomal protein L21
W: 60S ribosomal protein L17, putative
X: 60S ribosomal protein L22, putative
Y: 60S ribosomal protein L23
Z: 60S ribosomal protein L26, putative
0: 60S ribosomal protein L24, putative
1: 60S ribosomal protein L27
2: 60S ribosomal protein L28
3: 60S ribosomal protein L35, putative
4: 60S ribosomal protein L29, putative
5: 60S ribosomal protein L7, putative
6: 60S ribosomal protein L30e, putative
7: 60S ribosomal protein L31
8: 60S ribosomal protein L32
9: 60S ribosomal protein L35Ae, putative
a: 60S ribosomal protein L34
b: 60S ribosomal protein L36
c: Ribosomal protein L37
d: 60S ribosomal protein L38
e: 60S ribosomal protein L39
f: Ubiquitin-60S ribosomal protein L40
g: 60S ribosomal protein L41
h: 60S ribosomal protein L37a
i: 60S ribosomal protein L44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,136,616216
Polyers2,131,54645
Non-polymers5,070171
Water0
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (A2)406610
ΔGint (kcal/M)-4819
Surface area (A2)581500
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain28S ribosomal RNA


Mass: 1216212.125 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: GenBank: 1013064538
#2: RNA chain5S ribosomal RNA


Mass: 38410.859 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: GenBank: 1016052399
#3: RNA chain5.8S ribosomal RNA


Mass: 51206.461 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: GenBank: 1013064403

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLM...

#4: Polypeptide(L)60S ribosomal protein L2


Mass: 28064.998 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8I3T9

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)60S ribosomal protein L3 / 60S ribosomal protein L3 / putative


Mass: 44318.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IJC6

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)60S ribosomal protein L4


Mass: 46311.688 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8I431

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)60S ribosomal protein L11a, putative


Mass: 20268.666 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IBQ6
#8: Polypeptide(L)60S ribosomal protein L6, putative


Mass: 21638.562 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IE85
#9: Polypeptide(L)60S ribosomal protein L6-2, putative


Mass: 25587.623 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IDV1
#10: Polypeptide(L)60S ribosomal protein L7-3, putative


Mass: 32760.455 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ILL2

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)60S ribosomal protein L13, putative


Mass: 23805.344 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IJZ7

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)60S ribosomal protein L13


Mass: 25454.143 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IAX6
#13: Polypeptide(L)60S ribosomal protein L23, putative


Mass: 15015.713 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IE09
#14: Polypeptide(L)60S ribosomal protein L14, putative


Mass: 19340.373 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ILE8

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S ribosomal protein L27a, putative


Mass: 16765.834 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C6KT23
#17: Polypeptide(L)60S ribosomal protein L10, putative


Mass: 25265.480 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ILV2

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)60S ribosomal protein L5, putative


Mass: 34067.352 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ILL3

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)60S ribosomal protein L18-2, putative


Mass: 21508.783 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C0H5G3
#20: Polypeptide(L)60S ribosomal protein L19


Mass: 21641.096 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C6KSY6
#21: Polypeptide(L)60S ribosomal protein L18a


Mass: 21793.611 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IDS6
#22: Polypeptide(L)60S ribosomal protein L21 / 60S ribosomal protein L21e / putative


Mass: 18840.244 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ILK3

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)60S ribosomal protein L17, putative


Mass: 23469.926 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IDI5
#24: Polypeptide(L)60S ribosomal protein L22, putative


Mass: 16422.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IB51
#25: Polypeptide(L)60S ribosomal protein L23


Mass: 22152.748 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IE82
#26: Polypeptide(L)60S ribosomal protein L26, putative


Mass: 14855.709 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: O77364

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)60S ribosomal protein L24, putative


Mass: 19295.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IEM3
#28: Polypeptide(L)60S ribosomal protein L27 / 60S ribosomal protein L27 / putative


Mass: 16785.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IKM5

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)60S ribosomal protein L28 / 60S ribosomal protein L28 / putative


Mass: 14437.823 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IHU0

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)60S ribosomal protein L35, putative


Mass: 14787.824 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IIB4

Cellular component

Molecular function

Biological process

  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • translation (GO: 0006412)
#31: Polypeptide(L)60S ribosomal protein L29, putative / Ribosomal protein L29 / putative


Mass: 8041.588 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C6S3J6

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein L7, putative


Mass: 30593.184 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: O97250

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)60S ribosomal protein L30e, putative


Mass: 11794.760 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IJK8

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)60S ribosomal protein L31


Mass: 14099.854 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8I463

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein L32


Mass: 15565.751 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8I3B0

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)60S ribosomal protein L35Ae, putative / 60S ribosomal protein L35ae / putative


Mass: 16306.425 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IHT9

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein L34


Mass: 17406.967 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8IBY4
#38: Polypeptide(L)60S ribosomal protein L36


Mass: 12825.440 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8I713

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein L38 / 60S ribosomal protein L38e / putative


Mass: 10341.729 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8II62

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein L39


Mass: 6540.912 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C0H4H3
#43: Polypeptide(L)60S ribosomal protein L41 / 60S ribosomal protein L41 / putative


Mass: 5108.310 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C6S3G4

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein L37a


Mass: 10826.083 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: O96184

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein L44


Mass: 12194.902 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: O97231

Cellular component

Molecular function

Biological process

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Ribosomal protein ... , 2 types, 2 molecules Pc

#16: Polypeptide(L)Ribosomal protein L15


Mass: 24197.660 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C0H4A6
#39: Polypeptide(L)Ribosomal protein L37


Mass: 10571.592 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: C0H4L5

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Polypeptide(L) , 1 types, 1 molecules f

#42: Polypeptide(L)Ubiquitin-60S ribosomal protein L40


Mass: 14645.169 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum 3D7 / References: UniProt: Q8ID50

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Non-polymers , 3 types, 171 molecules

#46: ChemicalChemComp-YMZ / Mefloquine


Mass: 378.312 Da / Num. of mol.: 2 / Formula: C17H16F6N2O
#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 164 / Formula: Mg
#48: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Plasmodium falciparum 80S ribosome bound to mefloquine
Type: RIBOSOME
Buffer solutionDetails: 20 mM Hepes pH 7.4, 40 mM KAc, 10 mM NH4Ac, 10 mM Mg(Ac)2 and 5 mM 2-mecaptoethanol
Specimen supportDetails: Blot 2.5s before plunging / Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300
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 / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 90 K / Temperature (min): 80 K

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Processing

SoftwareName: REFMAC / Version: 5.8.0068 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0068
3D reconstructionResolution: 3.2 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43184
Atomic model buildingOverall b value: 129.3 / Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL
Refine

B iso mean: 129.307 A2 / Aniso B11: -0.25 A2 / Aniso B12: 0.09 A2 / Aniso B13: 0.15 A2 / Aniso B22: 0.17 A2 / Aniso B23: -0.02 A2 / Aniso B33: 0.08 A2 / Correlation coeff Fo to Fc: 0.952 / R factor R work: 0.27921 / R factor obs: 0.27921 / Highest resolution: 3.2 A / Lowest resolution: 257.5 A / Number reflection obs: 806977 / Percent reflection obs: 1 / Overall SU B: 29.102 / Overall SU ML: 0.428 / Overall ESU R: 0.567 / Solvent ion probe radii: 0.8 A / Solvent shrinkage radii: 0.8 A / Solvent vdw probe radii: 1.2 A / Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES / Solvent model details: MASK

Refine id
1
ELECTRON MICROSCOPY
Number of atoms included #1Total: 124503
Refine LS restraints
Refine idTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.014136485
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg0.8751.526196987
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg24.1856.9827685
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.18621.8972119
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.84215.00010690
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.95715.000538
ELECTRON MICROSCOPYr_chiral_restr0.3390.21322289
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02072478
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.34413.26824887
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it2.49619.89131002
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.19012.811111598
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined7.980518007
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.2 A / R factor R work: 0.576 / Lowest resolution: 3.283 A / Number reflection R free: 0 / Number reflection R work: 59775 / Total number of bins used: 20 / Percent reflection obs: 1

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