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- PDB-9t4r: Staphylococcus aureus 70S initiation complex with a natural mRNA -

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Basic information

Entry
Database: PDB / ID: 9t4r
TitleStaphylococcus aureus 70S initiation complex with a natural mRNA
Components
  • (Large ribosomal subunit protein ...) x 28
  • (Small ribosomal subunit protein ...) x 19
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Methionine tRNA
  • aur mRNA
KeywordsRIBOSOME / Shine-Delgarno / anti Shine-Delgarno / translation initiation / Staphylococcus aureus.
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / 5S rRNA binding / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / : / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28/L24 superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein S9, bacterial/plastid / Ribosomal L28 family / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S15, bacterial-type / L28p-like / : / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal L32p protein family / Ribosomal protein L21
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL33B / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsBahena Ceron, R. / Klaholz, B. / Marzi, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2026
Title: Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus.
Authors: Maximilian P Kohl / Roberto Bahena-Ceron / Béatrice Chane-Woon-Ming / Maria Kompatscher / Matthias D Erlacher / Charles Barchet / Ottilie von Loeffelholz / Pascale Romby / Bruno P Klaholz / Stefano Marzi /
Abstract: Regulation of translation initiation is central to bacterial adaptation, but species-specific mechanisms remain poorly understood. We present high-resolution mapping of translation start sites in ...Regulation of translation initiation is central to bacterial adaptation, but species-specific mechanisms remain poorly understood. We present high-resolution mapping of translation start sites in Staphylococcus aureus, revealing distinct features of initiation alongside numerous unannotated small ORFs. Our analysis, combined with cryo-EM of a native mRNA-ribosome complex, shows that S. aureus relies on extended, start codon proximal Shine-Dalgarno (SD) interactions, creating specificity against phylogenetically distant bacteria. Several natural S. aureus initiation sites are not correctly decoded by E. coli ribosomes. We identify new and conserved non-canonical start codons, whose regulatory initiation sites contain these characteristic extended SD sequence motifs. Finally, we characterize a novel example of uORF-mediated translational control in S. aureus, demonstrating that translation of a small leader peptide modulates expression of a key biofilm regulator. The described mechanism involves codon rarity, ribosome pausing, and arginine availability, linking nutrient sensing to biofilm formation in this major human pathogen.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL33B
X: aur mRNA
1: Large ribosomal subunit protein bL34
Z: Methionine tRNA
2: Large ribosomal subunit protein bL35
a: 23S rRNA
3: Large ribosomal subunit protein bL36
b: 5S rRNA
4: Large ribosomal subunit protein bL31B
c: Large ribosomal subunit protein uL2
A: 16S rRNA
d: Large ribosomal subunit protein uL3
B: Small ribosomal subunit protein uS2
e: Large ribosomal subunit protein uL4
C: Small ribosomal subunit protein uS3
f: Large ribosomal subunit protein uL5
D: Small ribosomal subunit protein uS4
g: Large ribosomal subunit protein uL6
E: Small ribosomal subunit protein uS5
j: Small ribosomal subunit protein uS10
F: Small ribosomal subunit protein bS6
k: Large ribosomal subunit protein uL15
G: Small ribosomal subunit protein uS7
l: Large ribosomal subunit protein uL16
H: Small ribosomal subunit protein uS8
m: Large ribosomal subunit protein bL17
I: Small ribosomal subunit protein uS9
n: Large ribosomal subunit protein uL18
J: Large ribosomal subunit protein uL13
o: Large ribosomal subunit protein bL19
K: Small ribosomal subunit protein uS11
p: Large ribosomal subunit protein bL20
L: Small ribosomal subunit protein uS12
q: Large ribosomal subunit protein bL21
M: Small ribosomal subunit protein uS13
r: Large ribosomal subunit protein uL22
N: Small ribosomal subunit protein uS14B
s: Large ribosomal subunit protein uL23
O: Small ribosomal subunit protein uS15
t: Large ribosomal subunit protein uL24
P: Small ribosomal subunit protein bS16
u: Large ribosomal subunit protein bL25
Q: Small ribosomal subunit protein uS17
v: Large ribosomal subunit protein bL27
R: Small ribosomal subunit protein bS18
w: Large ribosomal subunit protein bL28
S: Small ribosomal subunit protein uS19
x: Large ribosomal subunit protein uL29
T: Small ribosomal subunit protein bS20
y: Large ribosomal subunit protein uL30
U: Large ribosomal subunit protein uL14
z: Large ribosomal subunit protein bL32


Theoretical massNumber of molelcules
Total (without water)2,159,25352
Polymers2,159,25352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 28 types, 28 molecules 01234cdefgklmnJopqrstuvwxyUz

#1: Protein/peptide Large ribosomal subunit protein bL33B / 50S ribosomal protein L33 2


Mass: 5885.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FY22
#3: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 50S ribosomal protein L34 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FUQ0
#5: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FXQ0
#7: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW29
#9: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 9580.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FWD8
#10: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P60430
#12: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW06
#14: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW07
#16: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW18
#18: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19632.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A7X5E1
#22: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P0A0F8
#24: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW13
#26: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW33
#28: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13080.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW22
#29: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW38
#30: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FZ42
#32: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FXQ1
#34: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FXS8
#36: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW11
#38: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW08
#40: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 9839.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A7X5E7
#42: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0D1ICH8
#44: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FXT0
#46: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FZ60
#48: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW14
#50: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P0A0G2
#51: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW16
#52: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FZF1

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RNA chain , 5 types, 5 molecules XZabA

#2: RNA chain aur mRNA


Mass: 5594.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#4: RNA chain Methionine tRNA


Mass: 24497.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1848851804
#6: RNA chain 23S rRNA


Mass: 944650.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria)
#8: RNA chain 5S rRNA


Mass: 36975.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 2108766931
#11: RNA chain 16S rRNA


Mass: 500810.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1760139687

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Small ribosomal subunit protein ... , 19 types, 19 molecules BCDEjFGHIKLMNOPQRST

#13: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FZ25
#15: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW12
#17: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23023.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A7X3F0
#19: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW23
#20: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A6U3X6
#21: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2G113
#23: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17727.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P48940
#25: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW20
#27: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14727.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW39
#31: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13879.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW31
#33: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15376.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P0A0H0
#35: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW30
#37: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW19
#39: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2G2Q1
#41: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FZ45
#43: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW15
#45: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2G111
#47: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FW10
#49: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9012.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2FXY6

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S ribosome initiation complex / Type: COMPLEX
Entity ID: #1, #3, #5, #7, #9, #11, #13, #15, #17, #19, #21, #23, #25, #27, #29, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #2, #4, #6, #8, #10, #12, #14, #16, #18, #20, #22, #24, #26, ...Entity ID: #1, #3, #5, #7, #9, #11, #13, #15, #17, #19, #21, #23, #25, #27, #29, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #2, #4, #6, #8, #10, #12, #14, #16, #18, #20, #22, #24, #26, #28, #30, #32, #34, #36, #38, #40, #42, #44, #46, #48, #50, #52
Source: NATURAL
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
10cryoSPARC4.7.1initial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 316031 / Symmetry type: POINT

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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