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- PDB-5li0: 70S ribosome from Staphylococcus aureus -

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Entry
Database: PDB / ID: 5li0
Title70S ribosome from Staphylococcus aureus
Descriptor(30S ribosomal protein ...) x 19
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME / pathogenic ribosome / bL31 B-type / ribosome
Specimen sourceStaphylococcus aureus (strain nctc 8325) / bacteria
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsKhusainov, I. / Vicens, Q. / Bochler, A. / Grosse, F. / Myasnikov, A. / Menetret, J.F. / Chicher, J. / Marzi, S. / Romby, P. / Yusupova, G. / Yusupov, M. / Hashem, Y.
CitationNucleic Acids Res., 2016, 44, 10491-10504

Nucleic Acids Res., 2016, 44, 10491-10504 Yorodumi Papers
Structure of the 70S ribosome from human pathogen Staphylococcus aureus.
Iskander Khusainov / Quentin Vicens / Anthony Bochler / François Grosse / Alexander Myasnikov / Jean-François Ménétret / Johana Chicher / Stefano Marzi / Pascale Romby / Gulnara Yusupova / Marat Yusupov / Yaser Hashem

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2016 / Release: Dec 28, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 28, 2016Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collection / Derived calculationsem_software / struct_conn_em_software.name

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Assembly

Deposited unit
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14 type Z
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
A: 23S ribosomal RNA
B: 5S ribosomal RNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Y: 50S ribosomal protein L25
Z: 50S ribosomal protein L27
0: 50S ribosomal protein L28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L31 type B
4: 50S ribosomal protein L32
5: 50S ribosomal protein L33 2
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,097,74091
Polyers2,096,77750
Non-polymers96341
Water2,918162
#1


  • idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)242610
ΔGint (kcal/M)-2240
Surface area (Å2)785920
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules aAB

#1: RNA chain16S ribosomal RNA


Mass: 500464.406 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: GenBank: 87201381
#21: RNA chain23S ribosomal RNA


Mass: 945058.562 Da / Num. of mol.: 1
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325)
References: GenBank: 87201381
#22: RNA chain5S ribosomal RNA


Mass: 36692.801 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: GenBank: 87201381

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30S ribosomal protein ... , 19 types, 19 molecules bcdefghijk...

#2: Polypeptide(L)30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FZ25

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW12

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S4


Mass: 22920.221 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXK6

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S5


Mass: 17639.314 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW23

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6


Mass: 11368.879 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2G113

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S7


Mass: 17167.736 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: P48940

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S8


Mass: 14723.118 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW20

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S9


Mass: 14440.450 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW39

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#10: Polypeptide(L)30S ribosomal protein S10


Mass: 11600.520 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q931G5

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S11


Mass: 12562.294 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW31

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#12: Polypeptide(L)30S ribosomal protein S12


Mass: 15131.598 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q5HID0

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S13


Mass: 13487.543 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW30

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14 type Z


Mass: 7186.573 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW19

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S15


Mass: 10503.135 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2G2Q1

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S16


Mass: 10122.690 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FZ45

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S17


Mass: 10065.691 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW15

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S18


Mass: 8418.959 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2G111

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S19


Mass: 9605.988 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW10

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S20


Mass: 8708.018 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXY6

Cellular component

Molecular function

Biological process

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50S ribosomal protein ... , 28 types, 28 molecules DEFGHMNOPQ...

#23: Polypeptide(L)50S ribosomal protein L2


Mass: 29956.789 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: P60430

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L3


Mass: 23499.877 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW06

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L4


Mass: 21666.725 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW07

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L5


Mass: 18729.721 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW18

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L6


Mass: 18296.711 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW21

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW38

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW16

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L15


Mass: 14193.304 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: P0A0F8

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L16


Mass: 15943.755 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW13

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L17


Mass: 13420.350 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW33

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW22

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L19


Mass: 12594.825 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FZ42

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein L20


Mass: 13459.919 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXQ1

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXS8

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein L22


Mass: 12328.358 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW11

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein L23


Mass: 10380.100 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW08

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)50S ribosomal protein L24


Mass: 10976.878 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW17

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)50S ribosomal protein L25 / General stress protein CTC


Mass: 10522.318 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2G0S0

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)50S ribosomal protein L27


Mass: 8911.099 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXT0

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein L28


Mass: 5312.262 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FZ60

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)50S ribosomal protein L29


Mass: 7660.762 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW14

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein L30


Mass: 6305.308 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: P0A0G2

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FWD8

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)50S ribosomal protein L32


Mass: 6397.427 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FZF1

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)50S ribosomal protein L33 2


Mass: 4711.371 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FY22

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)50S ribosomal protein L34


Mass: 5323.446 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FUQ0

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)50S ribosomal protein L35


Mass: 6985.402 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FXQ0

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (strain NCTC 8325) / References: UniProt: Q2FW29

Cellular component

Molecular function

Biological process

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Non-polymers , 4 types, 203 molecules

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


Mass: 24.305 Da / Num. of mol.: 31 / Formula: Mg
#52: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 9 / Formula: O
#53: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn
#54: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 70S ribosome from Staphylococcus aureus / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
Source (natural)Organism: Staphylococcus aureus (strain NCTC 8325)
Buffer solutionDetails: 5 mM Hepes-KOH pH 7.5 50 mM KCl 10 mM NH4Cl 10 mM Mg(OAc)2 1 mM DTT
pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot force 5, blot waiting time 30 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingAverage exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3850
Image scansMovie frames/image: 17 / Used frames/image: 2-8

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Processing

SoftwareName: PHENIX / Version: dev_2341: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1Xmipp3PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7VMD1.9.2MODEL FITTING1
8NAMD2MODEL FITTING1
10PHENIX1.10.1-2155MODEL REFINEMENT1
11PHENIXdev-2341MODEL REFINEMENT1
12Erraser1.10.1-2155MODEL REFINEMENT1
13RELION1.3INITIAL EULER ASSIGNMENT1
14RELION1.3FINAL EULER ASSIGNMENT1
15RELION1.3CLASSIFICATION1
16RELION1.3RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 423497
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 110000 / Algorithm: FOURIER SPACE / Number of class averages: 8 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011246899
ELECTRON MICROSCOPYf_angle_d1.183443889
ELECTRON MICROSCOPYf_dihedral_angle_d17.669107275
ELECTRON MICROSCOPYf_chiral_restr0.05529332
ELECTRON MICROSCOPYf_plane_restr0.00621135

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