5LI0

70S ribosome from Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the 70S ribosome from human pathogen Staphylococcus aureus.

Khusainov, I.Vicens, Q.Bochler, A.Grosse, F.Myasnikov, A.Menetret, J.F.Chicher, J.Marzi, S.Romby, P.Yusupova, G.Yusupov, M.Hashem, Y.

(2016) Nucleic Acids Res. 44: 10491-10504

  • DOI: 10.1093/nar/gkw933

  • PubMed Abstract: 
  • Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the imp ...

    Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance. Here, we present the first full 70S ribosome structure from Staphylococcus aureus, a Gram-positive pathogenic bacterium, solved by cryo-electron microscopy. Comparative analysis with other known bacterial ribosomes pinpoints several unique features specific to S. aureus around a conserved core, at both the protein and the RNA levels. Our work provides the structural basis for the many studies aiming at understanding translation regulation in S. aureus and for designing drugs against this often multi-resistant pathogen.


    Organizational Affiliation

    Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch 67400, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
255Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsB
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ25
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
217Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsC
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW12
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
199Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsD
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXK6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
165Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW23
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
96Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G113
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
150Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P48940
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
131Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsH
Find proteins for Q2FW20 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW20
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
128Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsI
Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW39
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
102Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q931G5 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  Q931G5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
118Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsK
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW31
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
135Staphylococcus aureus (strain COL)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5HID0 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HID0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsM
Find proteins for Q2FW30 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW30
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
60Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsZ (rpsN1)
Find proteins for Q2FW19 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW19
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
88Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G2Q1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
90Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ45
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
86Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW15
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
71Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G111
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
84Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW10
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
80Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpsT
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXY6
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
D
275Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
E
218Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
F
199Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
G
166Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
H
164Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplF
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
M
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
N
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
O
131Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
P
141Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Q
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
R
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
S
110Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
T
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
U
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
V
112Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
W
89Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
X
100Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Y
94Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0S0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
Z
82Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
0
46Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
1
65Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
2
57Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
3
84Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmE2
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FWD8
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
4
56Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmF
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 2
5
39Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmG2
Find proteins for Q2FY22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FY22
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
6
44Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
7
60Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
8
37Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1547Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 21
MoleculeChainsLengthOrganism
23S ribosomal RNAA2918Staphylococcus aureus subsp. aureus NCTC 8325
Entity ID: 22
MoleculeChainsLengthOrganism
5S ribosomal RNAB114Staphylococcus aureus subsp. aureus NCTC 8325
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
8
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download SDF File 
Download CCD File 
A
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
a, A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Derived calculations