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- PDB-9ebb: Cryo-EM structure of the MPY and ribosome-tunnel occluding hibern... -

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Basic information

Entry
Database: PDB / ID: 9ebb
TitleCryo-EM structure of the MPY and ribosome-tunnel occluding hibernation factors bound to the Mycobacterium tuberculosis C- 70S ribosome
Components
  • (30S ribosomal protein ...) x 16
  • (50S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 4
  • (Small ribosomal subunit protein ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • DUF5302 domain-containing protein
  • Mitochondrial domain of uncharacterized function (DUF1713)
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / hibernating ribosome / Mycobacterium tuberculosis / nascent peptide exit tunnel / 70S / hibernation factor / Mpy / TRANSLATION
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit ...negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF5302 / Family of unknown function (DUF5302) / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein ...Protein of unknown function DUF5302 / Family of unknown function (DUF5302) / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / 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 L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S6, plastid/chloroplast / : / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Uncharacterized protein Rv1155A / Ribosome hibernation promoting factor / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / : / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMajumdar, S. / Ojha, A.K. / Agrawal, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32422 United States
CitationJournal: Biorxiv / Year: 2024
Title: A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis
Authors: Majumdar, S. / Li, Y. / Manjari, S.R. / Gamper, H.B. / Hou, Y.M. / Banavali, N.K. / Ojha, A.K. / Agrawal, R.K.
History
DepositionNov 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
b: Large ribosomal subunit protein bL33
1: DUF5302 domain-containing protein
0: 50S ribosomal protein L32
2: 50S ribosomal protein bL34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
I: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: Large ribosomal subunit protein uL14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: Large ribosomal subunit protein bL21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 16S ribosomal RNA
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
x: Mitochondrial domain of uncharacterized function (DUF1713)
A: Ribosome hibernation promoting factor
r: Small ribosomal subunit protein bS18
9: Small ribosomal subunit protein uS14
y: Large ribosomal subunit protein bL28
7: 50S ribosomal protein bL37


Theoretical massNumber of molelcules
Total (without water)2,277,25954
Polymers2,277,25954
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 ... , 4 types, 4 molecules bKRy

#1: Protein Large ribosomal subunit protein bL33


Mass: 6604.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JMX7
#17: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13451.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: P66070
#24: Protein Large ribosomal subunit protein bL21


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A2I7W9M4
#53: Protein Large ribosomal subunit protein bL28


Mass: 9117.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JNK5

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Protein , 2 types, 2 molecules 1A

#2: Protein DUF5302 domain-containing protein


Mass: 6810.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A089QKZ7
#50: Protein Ribosome hibernation promoting factor / HPF


Mass: 24579.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0E8WVX4

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50S ribosomal protein ... , 26 types, 26 molecules 02346CDEFGHJLMNOPQSTUVWYZ7

#3: Protein 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IMI5
#4: Protein/peptide 50S ribosomal protein bL34 / Large ribosomal subunit protein bL34


Mass: 5643.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: P0A5W5
#5: Protein 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KKY9
#6: Protein/peptide 50S ribosomal protein L36


Mass: 4355.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#7: Protein 50S ribosomal protein L31


Mass: 8770.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HLX7
#10: Protein 50S ribosomal protein L2


Mass: 30644.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H5T7
#11: Protein 50S ribosomal protein L3


Mass: 23127.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU18
#12: Protein 50S ribosomal protein L4


Mass: 23779.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9H1
#13: Protein 50S ribosomal protein L5


Mass: 21052.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUU0
#14: Protein 50S ribosomal protein L6


Mass: 19408.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJU1
#15: Protein 50S ribosomal protein L9


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW48
#16: Protein 50S ribosomal protein L13


Mass: 21646.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T9D5H2
#18: Protein 50S ribosomal protein L15


Mass: 15566.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWY0
#19: Protein 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWV9
#20: Protein 50S ribosomal protein L17


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IVA2
#21: Protein 50S ribosomal protein L18


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JK28
#22: Protein 50S ribosomal protein L19


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDD2
#23: Protein 50S ribosomal protein L20


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85
#25: Protein 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H760
#26: Protein 50S ribosomal protein L23


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9M3
#27: Protein 50S ribosomal protein L24


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXU4
#28: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JAK4
#29: Protein 50S ribosomal protein L27


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045K0G1
#30: Protein 50S ribosomal protein L29


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IQ64
#31: Protein 50S ribosomal protein L30


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2
#54: Protein/peptide 50S ribosomal protein bL37


Mass: 2882.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0AB73YSK1

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RNA chain , 3 types, 3 molecules IBa

#8: RNA chain 23S ribosomal RNA


Mass: 1017792.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 984989958
#9: RNA chain 5S ribosomal RNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771551
#32: RNA chain 16S ribosomal RNA


Mass: 498260.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1050844762

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30S ribosomal protein ... , 16 types, 16 molecules cdefghijklmopqst

#33: Protein 30S ribosomal protein S3


Mass: 30071.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4H6
#34: Protein 30S ribosomal protein S4


Mass: 23515.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GRS4
#35: Protein 30S ribosomal protein S5


Mass: 22925.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JKV0
#36: Protein 30S ribosomal protein S6


Mass: 10952.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JVY9
#37: Protein 30S ribosomal protein S7


Mass: 17633.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JMN7
#38: Protein 30S ribosomal protein S8


Mass: 14432.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWX2
#39: Protein 30S ribosomal protein S9


Mass: 16465.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I839
#40: Protein 30S ribosomal protein S10


Mass: 11452.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HTN2
#41: Protein 30S ribosomal protein S11


Mass: 14815.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045I821
#42: Protein 30S ribosomal protein S12


Mass: 13882.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: M9TET4
#43: Protein 30S ribosomal protein S13


Mass: 14383.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GT82
#44: Protein 30S ribosomal protein S15


Mass: 10500.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JF49
#45: Protein 30S ribosomal protein S16


Mass: 17466.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JER3
#46: Protein 30S ribosomal protein S17


Mass: 14776.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0E9AP91
#47: Protein 30S ribosomal protein S19


Mass: 10830.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXT2
#48: Protein 30S ribosomal protein S20


Mass: 9428.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045GXQ2

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Protein/peptide , 1 types, 1 molecules x

#49: Protein/peptide Mitochondrial domain of uncharacterized function (DUF1713)


Mass: 4178.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)

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Small ribosomal subunit protein ... , 2 types, 2 molecules r9

#51: Protein Small ribosomal subunit protein bS18


Mass: 9714.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JGY8
#52: Protein Small ribosomal subunit protein uS14


Mass: 11471.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJ13

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Details

Has protein modificationN

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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: Mycobacterium tuberculosis C- 70S ribosomal subunit bound to the ribosome-tunnel occluding hibernation factor, RTOF and the ribosome hibernation promoting factor, Mpy
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5 / Details: Polymix buffer
Buffer component
IDConc.NameFormulaBuffer-ID
195 mMPotassium chlorideKCl1
25 mMAmmonum chlorideNH4Cl1
35 mMMagnesium acetateMg(OAC)21
40.5 mMCalcium chlorideCaCl21
58 mMPutrescine1
61 mMSpermidine1
75 mMPotassium phosphateKP1
81 mMDithiotreitol1
SpecimenConc.: 0.3 mg/ml / Embedding 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

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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 magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 0.001 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13499

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.0particle selection
2Leginonimage acquisition
4cryoSPARCv4.4.0CTF correction
10cryoSPARCv4.4.0final Euler assignment
11cryoSPARCv4.4.0classification
12cryoSPARCv4.4.03D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5471811
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25583 / Symmetry type: POINT
Atomic model buildingB value: 48.6 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-corelation coefficient
Atomic model buildingPDB-ID: 7MT7

7mt7


Accession code: 7MT7 / Source name: PDB / Type: experimental model

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  • 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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