6FXC

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.

Matzov, D.Aibara, S.Basu, A.Zimmerman, E.Bashan, A.Yap, M.F.Amunts, A.Yonath, A.E.

(2017) Nat Commun 8: 723-723

  • DOI: 10.1038/s41467-017-00753-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gr ...

    Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.


    Organizational Affiliation

    Faculty of Chemistry, Department of Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel. ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
Ac, Bc
202Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsCSAB2116c
Find proteins for Q2YYQ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ2

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
Ad, Bd
198Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsDSAB1578
Find proteins for Q2YTH0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTH0

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
Ae, Be
156Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsESAB2105c
Find proteins for Q2YYL4 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL4

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
Ag, Bg
152Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077VHU6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VHU6

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
Ah, Bh
131Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsHSAB2108c
Find proteins for Q2YYL1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL1

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
Ai, Bi
127Staphylococcus aureusMutation(s): 0 
Gene Names: rpsIBTN44_13505EP54_02240EQ90_01125
Find proteins for A0A1Q4GY48 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q4GY48

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
Aj, Bj
97Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsJSAB2123c
Find proteins for Q2YYP5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP5

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
Ak, Bk
114Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsKSAB2098c
Find proteins for Q2YYM1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM1

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
Al, Bl
135Staphylococcus aureusMutation(s): 0 
Gene Names: rpsLHMPREF3211_01391
Find proteins for A0A133PZQ5 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PZQ5

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
Am, Bm
121Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsMSAB2099c
Find proteins for Q2YYM0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM0

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
An, Bn
60Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsZrpsN1SAB2109c
Find proteins for Q2YYL0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL0

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
Ao, Bo
88Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsOSAB1135
Find proteins for Q2YXP3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXP3

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
Ap, Bp
89Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsPSAB1102
Find proteins for Q2YXH8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXH8

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Aq, Bq
80Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsQSAB2113c
Find proteins for Q2YYK6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK6

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
Ar, Br
54Staphylococcus aureusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
As, Bs
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsSHMPREF3211_01571
Find proteins for A0A133PYC3 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PYC3

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
At, Bt
81Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsTSAB1458
Find proteins for Q2YT41 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT41

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
Au, Bu
52Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsUSAB1447c
Find proteins for Q2YT04 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT04

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
Av, Bv
190Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: hpfSAB0704
Find proteins for Q2YSH7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YSH7

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AC, BC
274Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplBSAB2119c
Find proteins for Q2YYP9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP9

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AE, BE
206Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplDSAB2121c
Find proteins for Q2YYP7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AG, BG
175Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplFSAB2107c
Find proteins for Q2YYL2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL2

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AH, BH
145Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplMSAB2091c
Find proteins for Q2YYM8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM8

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AI, BI
122Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplNSAB2112c
Find proteins for Q2YYK7 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK7

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AJ, BJ
146Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplOSAB2103c
Find proteins for Q2YYL6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL6

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AK, BK
137Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplPSAB2115c
Find proteins for Q2YYQ3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ3

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AL, BL
120Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplQSAB2096c
Find proteins for Q2YYM3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYM3

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AM, BM
119Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AN, BN
114Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplSSAB1105
Find proteins for Q2YXM4 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXM4

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AO, BO
116Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplTSAB1538c
Find proteins for Q2YTB1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTB1

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AP, BP
102Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplUSAB1516c
Find proteins for Q2YT83 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YT83

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AQ, BQ
112Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplVSAB2117c
Find proteins for Q2YYQ1 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYQ1

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AR, BR
89Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplWSAB2120c
Find proteins for Q2YYP8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP8

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AS, BS
103Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplXSAB2111c
Find proteins for Q2YYK8 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK8

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AT, BT
94Staphylococcus aureusMutation(s): 0 
Gene Names: rplYctcHMPREF3211_00359SAKG03_04770
Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
Go to UniProtKB:  A0A133Q8Z9

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AV, BV
58Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmBSAB1088c
Find proteins for Q2YXJ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXJ2

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
AW, BW
67Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmCSAB2114c
Find proteins for Q2YYN0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYN0

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
AX, BX
58Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmDSAB2104c
Find proteins for Q2YYL5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYL5

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
AY, BY
59Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmE2SAB2004c
Find proteins for Q2YUN3 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YUN3

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
AZ, BZ
48Staphylococcus aureusMutation(s): 0 
Gene Names: rpmFBSZ10_12860
Find proteins for A0A1Q8DAT0 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q8DAT0

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A1, B1
47Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077V2P0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V2P0

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A2, B2
43Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmHSAB2590c
Find proteins for Q2YZB6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YZB6

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A3, B3
64Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpmISAB1539c
Find proteins for Q2YTB0 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YTB0

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A4, B4
37Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
Ab, Bb
226Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsBSAB1118
Find proteins for Q2YXL2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YXL2

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AD, BD
215Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplCSAB2122c
Find proteins for Q2YYP6 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYP6

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AF, BF
175Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rplESAB2110c
Find proteins for Q2YYK9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YYK9

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AU, BU
82Staphylococcus aureusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
Af, Bf
95Staphylococcus aureus (strain bovine RF122 / ET3-1)Mutation(s): 0 
Gene Names: rpsFSAB0316
Find proteins for Q2YVJ2 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YVJ2

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAa, Ba1539Staphylococcus aureus

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Entity ID: 23
MoleculeChainsLengthOrganism
23S ribosomal RNAAA, BA2923Staphylococcus aureus

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Entity ID: 24
MoleculeChainsLengthOrganism
5S ribosomal RNAAB, BB115Staphylococcus aureus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSwedenFFL15-0325
European Research CouncilIsrael322581

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations