5ND8

Hibernating ribosome from Staphylococcus aureus (Unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.

Khusainov, I.Vicens, Q.Ayupov, R.Usachev, K.Myasnikov, A.Simonetti, A.Validov, S.Kieffer, B.Yusupova, G.Yusupov, M.Hashem, Y.

(2017) EMBO J 36: 2073-2087

  • DOI: 10.15252/embj.201696105
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structu ...

    In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials.


    Organizational Affiliation

    CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France marat@igbmc.fr y.hashem@ibmc-cnrs.unistra.fr.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Find proteins for A7X5G6 (Staphylococcus aureus (strain Mu3 / ATCC 700698))
Go to UniProtKB:  A7X5G6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
129Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsKSAOUHSC_02486
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW31
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
137Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsLSAOUHSC_00527
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0H0
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
121Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsMSAOUHSC_02487
Find proteins for Q2FW30 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW30
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsZrpsN1SAOUHSC_02499
Find proteins for Q2FW19 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW19
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsOSAOUHSC_01250
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G2Q1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsPSAOUHSC_01208
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ45
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
87Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsQSAOUHSC_02503
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW15
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsRSAOUHSC_00350
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G111
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
92Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsSSAOUHSC_02508
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW10
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsBSAOUHSC_01232
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ25
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsTSAOUHSC_01689
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXY6
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsUSAOUHSC_01678
Find proteins for Q2FXZ7 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXZ7
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
v
190Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: hpfSAOUHSC_00767
Find proteins for Q2G055 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G055
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
D
277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
E
220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
F
207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
G
179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW18
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
H
178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW21
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsCSAOUHSC_02506
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW12
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
M
145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
N
122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
O
146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
P
144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Q
122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
R
119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
S
116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
T
118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
U
102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
V
117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsDSAOUHSC_01829
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXK6
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
W
91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
X
105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
Y
217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G0S0
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
Z
94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
0
62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
1
69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
2
59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
3
84Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmE2SAOUHSC_02361
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FWD8
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
4
58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 2
5
49Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmG2SAOUHSC_01651
Find proteins for Q2FY22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FY22
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsESAOUHSC_02494
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW23
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
6
45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
7
66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
8
37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmJSAOUHSC_02488
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
98Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsFSAOUHSC_00348
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G113
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsGSAOUHSC_00528
Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P48940
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsHSAOUHSC_02498
Find proteins for Q2FW20 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW20
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsISAOUHSC_02477
Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW39
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAa1547Staphylococcus aureus subsp. aureus NCTC 8325

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Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAA2918Staphylococcus aureus subsp. aureus NCTC 8325

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Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAB114Staphylococcus aureus subsp. aureus NCTC 8325
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-10-LABX-0036_NETRNA
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheFranceANR-15-CE11-0021-01
Russian Science FoundationRussian Federation16-14-10014
European Research Council294312
French National Research AgencyFranceFDT20140930867

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references, Other
  • Version 1.2: 2017-07-26
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-02-20
    Changes: Advisory, Author supporting evidence, Data collection, Derived calculations
  • Version 1.5: 2019-11-06
    Changes: Data collection
  • Version 1.6: 2019-12-11
    Changes: Other