[English] 日本語
Yorodumi
- PDB-9e0n: M. smegmatis unmethylated 70S ribosome structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e0n
TitleM. smegmatis unmethylated 70S ribosome structure
Components
  • (50S ribosomal protein ...) x 3
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 19
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Conserved domain protein
KeywordsRIBOSOME / 70S ribosome / unmethylated ribosome / ribonucleoprotein complex / protein synthesis
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / : / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / : / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L6, 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 L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Conserved domain protein / Large ribosomal subunit protein bL33A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Conserved domain protein / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / 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 uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsNandi, S. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI088025 United States
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Distant ribose 2'-O-methylation of 23S rRNA helix 69 pre-orders the capreomycin drug binding pocket at the ribosome subunit interface.
Authors: Suparno Nandi / Debayan Dey / Pooja Srinivas / Christine M Dunham / Graeme L Conn /
Abstract: Loss of ribosomal RNA (rRNA) modifications incorporated by the intrinsic methyltransferase TlyA results in reduced sensitivity to tuberactinomycin antibiotics such as capreomycin. However, how rRNA ...Loss of ribosomal RNA (rRNA) modifications incorporated by the intrinsic methyltransferase TlyA results in reduced sensitivity to tuberactinomycin antibiotics such as capreomycin. However, how rRNA methylation alters drug binding, particularly at the distant but functionally more important site in 23S rRNA helix 69 (H69), is currently unknown. We determined high-resolution cryo-electron microscopy structures of the Mycolicibacterium smegmatis 70S ribosome with or without the two ribose 2'-O-methyl modifications incorporated by TlyA. In the unmodified ribosome, the tip of H69 adopts a more compact conformation, positioning two key nucleotides (A2137 and C2138) such that interactions with capreomycin would be lost and the binding pocket partially occluded. Methylation of 23S rRNA nucleotide C2144 promotes conformational changes that result in a more favorable positioning of C2138 and adoption of a more open conformation to enable capreomycin binding. Molecular dynamics simulations and H69 RNA helical analyses additionally reveal specific propagation of these changes from the site of modification to the H69 tip, allosterically reconfiguring the capreomycin binding site. Methylation of h44 also results in structural rearrangements at the H69-h44 interface to support maintenance of these changes that favor antibiotic binding. This work thus reveals the effect and regulation of distant rRNA methylation on ribosome-targeting antibiotic binding.
History
DepositionOct 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Large ribosomal subunit protein uL30
2: Large ribosomal subunit protein bL31
3: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL33A
5: Large ribosomal subunit protein bL34
6: Large ribosomal subunit protein bL35
7: 50S ribosomal protein L36
8: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: 50S ribosomal protein L9
I: Large ribosomal subunit protein uL10
J: Large ribosomal subunit protein uL11
K: Large ribosomal subunit protein uL13
L: Large ribosomal subunit protein uL14
M: Large ribosomal subunit protein uL15
N: Large ribosomal subunit protein uL16
O: Large ribosomal subunit protein bL17
P: Large ribosomal subunit protein uL18
Q: Large ribosomal subunit protein bL19
R: Large ribosomal subunit protein bL20
S: Large ribosomal subunit protein bL21
T: Large ribosomal subunit protein uL22
U: Large ribosomal subunit protein uL23
V: Large ribosomal subunit protein uL24
W: Large ribosomal subunit protein bL25
X: Large ribosomal subunit protein bL27
Y: Large ribosomal subunit protein bL28
Z: Large ribosomal subunit protein uL29
a: 16S rRNA
b: Small ribosomal subunit protein uS2
c: Small ribosomal subunit protein uS3
d: Small ribosomal subunit protein uS4
e: Small ribosomal subunit protein uS5
f: Small ribosomal subunit protein bS6
g: Small ribosomal subunit protein uS7
h: Small ribosomal subunit protein uS8
i: Small ribosomal subunit protein uS9
j: Small ribosomal subunit protein uS10
k: Small ribosomal subunit protein uS11
l: Small ribosomal subunit protein uS12
m: Small ribosomal subunit protein uS13
n: Small ribosomal subunit protein uS14B
o: Small ribosomal subunit protein uS15
p: Small ribosomal subunit protein bS16
q: Small ribosomal subunit protein uS17
r: Small ribosomal subunit protein bS18B
s: Small ribosomal subunit protein uS19
t: Small ribosomal subunit protein bS20
u: Conserved domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,280,004162
Polymers2,277,40355
Non-polymers2,601107
Water00
1


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

-
Components

+
Large ribosomal subunit protein ... , 29 types, 29 molecules 123456CDEFGIJKLMNOPQRSTUVWXYZ

#1: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG7
#2: Protein Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R215
#3: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R3I9
#4: Protein Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QS39
#5: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R7K0
#6: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QYU7
#11: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD4
#12: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD1
#13: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD2
#14: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG1
#15: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG4
#17: Protein Large ribosomal subunit protein uL10 / 50S ribosomal protein L10


Mass: 17964.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QS62
#18: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QS45
#19: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSP8
#20: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSF9
#21: Protein Large ribosomal subunit protein uL15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG8
#22: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD8
#23: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 19210.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSL9
#24: Protein Large ribosomal subunit protein uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG5
#25: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QV42
#26: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QYU6
#27: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R151
#28: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD6
#29: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD3
#30: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG0
#31: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R3D2
#32: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R150
#33: Protein Large ribosomal subunit protein bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QV03
#34: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD9

-
50S ribosomal protein ... , 3 types, 3 molecules 78H

#7: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSL4
#8: Protein/peptide 50S ribosomal protein bL37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QTP4
#16: Protein 50S ribosomal protein L9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A653F9J9

-
RNA chain , 3 types, 3 molecules ABa

#9: RNA chain 23S rRNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: GenBank: 2198294598
#10: RNA chain 5S rRNA


Mass: 38038.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: GenBank: 2093960070
#35: RNA chain 16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: GenBank: 2093960070

-
Small ribosomal subunit protein ... , 19 types, 19 molecules bcdefghijklmnopqrst

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


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QVB8
#37: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD7
#38: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSL7
#39: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG6
#40: Protein Small ribosomal subunit protein bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0A2U9Q0X2
#41: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QS97
#42: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG3
#43: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSP9
#44: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD0
#45: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSL6
#46: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QS96
#47: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSL5
#48: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSG2
#49: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QVQ3
#50: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QV37
#51: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSE0
#52: Protein Small ribosomal subunit protein bS18B / 30S ribosomal protein S18 2


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R7F7
#53: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QSD5
#54: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0R102

-
Protein/peptide / Non-polymers , 2 types, 108 molecules u

#55: Protein/peptide Conserved domain protein


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A / References: UniProt: A0QR10
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 107 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: M. smegmatis unmethylated 70S ribosome / Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: LR222 C101A
Buffer solutionpH: 7.6
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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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: 2100 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2 sec. / Electron dose: 52.51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5060
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7Coot0.9.8.1model fitting
9PHENIX1.17.1_3660model refinement
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227969 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 5ZEB

5zeb


Accession code: 5ZEB / Source name: PDB / Type: experimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more