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- PDB-8r55: Bacillus subtilis MutS2-collided disome complex (collided 70S) -

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Basic information

Entry
Database: PDB / ID: 8r55
TitleBacillus subtilis MutS2-collided disome complex (collided 70S)
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 6
  • (Large ribosomal subunit protein ...) x 21
  • 16S rRNA (1533-MER)
  • 23S RNA (2887-MER)
  • 5S rRNA (112-MER)
  • Endonuclease MutS2
  • mRNA (33-MER)
  • tRNA (73-MER)
  • tRNA (77-MER)
KeywordsRIBOSOME / Muts2 / collision / disome / splitting / quality control
Function / homology
Function and homology information


mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / mismatch repair / large ribosomal subunit / small ribosomal subunit / transferase activity / endonuclease activity / tRNA binding / Hydrolases; Acting on ester bonds ...mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / mismatch repair / large ribosomal subunit / small ribosomal subunit / transferase activity / endonuclease activity / tRNA binding / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ATP hydrolysis activity / zinc ion binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal ...MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / Type-1 KH domain profile. / Ribosomal protein S14, type Z / 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 L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS7 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL6 / Endonuclease MutS2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsPark, E. / Mackens-Kiani, T. / Berhane, R. / Esser, H. / Erdenebat, C. / Burroughs, A.M. / Berninghausen, O. / Aravind, L. / Beckmann, R. / Green, R. / Buskirk, A.R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR174 Germany
CitationJournal: EMBO J / Year: 2024
Title: B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage.
Authors: Esther N Park / Timur Mackens-Kiani / Rebekah Berhane / Hanna Esser / Chimeg Erdenebat / A Maxwell Burroughs / Otto Berninghausen / L Aravind / Roland Beckmann / Rachel Green / Allen R Buskirk /
Abstract: Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the ...Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains, and we reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation through the ribosome quality control pathway. However, unlike SmrB, which cleaves mRNA in E. coli, we see no evidence that MutS2 mediates mRNA cleavage or promotes ribosome rescue by tmRNA. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in diverse bacteria.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 28, 2024Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: Large ribosomal subunit protein bL33
2: Large ribosomal subunit protein bL34
3: Large ribosomal subunit protein bL35
4: 50S ribosomal protein L36
6: Large ribosomal subunit protein bL31
7: tRNA (73-MER)
A: 16S rRNA (1533-MER)
B: 30S ribosomal protein S2
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
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: tRNA (77-MER)
V: mRNA (33-MER)
Y: 5S rRNA (112-MER)
Z: Large ribosomal subunit protein uL2
a: Large ribosomal subunit protein uL3
b: Large ribosomal subunit protein uL4
c: Large ribosomal subunit protein uL5
d: Large ribosomal subunit protein uL6
e: Large ribosomal subunit protein uL13
f: 50S ribosomal protein L14
i: 50S ribosomal protein L15
j: Large ribosomal subunit protein uL16
k: Large ribosomal subunit protein bL17
l: 50S ribosomal protein L18
m: 50S ribosomal protein L19
n: Large ribosomal subunit protein bL20
o: Large ribosomal subunit protein bL21
r: Large ribosomal subunit protein uL22
s: Large ribosomal subunit protein uL23
t: Large ribosomal subunit protein uL24
u: Large ribosomal subunit protein bL27
v: Large ribosomal subunit protein bL28
w: Large ribosomal subunit protein uL29
x: Large ribosomal subunit protein uL30
X: 23S RNA (2887-MER)
z: Endonuclease MutS2


Theoretical massNumber of molelcules
Total (without water)2,241,42053
Polymers2,241,42053
Non-polymers00
Water0
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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50S ribosomal protein ... , 6 types, 6 molecules 04film

#1: Protein 50S ribosomal protein L32 /


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I502
#5: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A199WAC7
#37: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X754
#38: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCP1
#41: Protein 50S ribosomal protein L18 /


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS9
#42: Protein 50S ribosomal protein L19 /


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XHU6

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Large ribosomal subunit protein ... , 21 types, 21 molecules 1236Zabcdejknorstuvwx

#2: Protein/peptide Large ribosomal subunit protein bL33


Mass: 5786.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I267
#3: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCT1
#4: Protein Large ribosomal subunit protein bL35


Mass: 7597.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XFQ7
#6: Protein Large ribosomal subunit protein bL31


Mass: 7216.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XD11
#31: Protein Large ribosomal subunit protein uL2


Mass: 30074.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCB6
#32: Protein Large ribosomal subunit protein uL3


Mass: 22462.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X745
#33: Protein Large ribosomal subunit protein uL4


Mass: 22222.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X8U6
#34: Protein Large ribosomal subunit protein uL5


Mass: 20046.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB64
#35: Protein Large ribosomal subunit protein uL6


Mass: 19124.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A857HBB3
#36: Protein Large ribosomal subunit protein uL13


Mass: 16017.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCH0
#39: Protein Large ribosomal subunit protein uL16


Mass: 15619.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB41
#40: Protein Large ribosomal subunit protein bL17


Mass: 13643.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCG5
#43: Protein Large ribosomal subunit protein bL20


Mass: 13408.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XFC1
#44: Protein Large ribosomal subunit protein bL21


Mass: 11164.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XIS2
#45: Protein Large ribosomal subunit protein uL22


Mass: 12035.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRT3
#46: Protein Large ribosomal subunit protein uL23


Mass: 10778.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XB36
#47: Protein Large ribosomal subunit protein uL24


Mass: 10921.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRS7
#48: Protein Large ribosomal subunit protein bL27


Mass: 8956.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XF22
#49: Protein Large ribosomal subunit protein bL28


Mass: 6367.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XHT6
#50: Protein Large ribosomal subunit protein uL29


Mass: 7598.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRV8
#51: Protein Large ribosomal subunit protein uL30


Mass: 6519.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRU6

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RNA chain , 6 types, 6 molecules 7AUVYX

#7: RNA chain tRNA (73-MER)


Mass: 23545.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1851743410
#8: RNA chain 16S rRNA (1533-MER)


Mass: 496854.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1864548803
#28: RNA chain tRNA (77-MER)


Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1772258810
#29: RNA chain mRNA (33-MER)


Mass: 10591.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria)
#30: RNA chain 5S rRNA (112-MER)


Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 1560663034
#52: RNA chain 23S RNA (2887-MER)


Mass: 949646.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: GenBank: 2038422476

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30S ribosomal protein ... , 19 types, 19 molecules BCDEFGHIJKLMNOPQRST

#9: Protein 30S ribosomal protein S2 /


Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XFB4
#10: Protein 30S ribosomal protein S3 /


Mass: 24351.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3N6BZP3
#11: Protein 30S ribosomal protein S4 /


Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XDX5
#12: Protein 30S ribosomal protein S5 /


Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A1A0G5K9
#13: Protein 30S ribosomal protein S6 /


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCU1
#14: Protein 30S ribosomal protein S7 /


Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X741
#15: Protein 30S ribosomal protein S8 /


Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCN0
#16: Protein 30S ribosomal protein S9 /


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCS1
#17: Protein 30S ribosomal protein S10 /


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRV5
#18: Protein 30S ribosomal protein S11 /


Mass: 13993.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A7U5HS75
#19: Protein 30S ribosomal protein S12 /


Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCJ2
#20: Protein 30S ribosomal protein S13 /


Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063X7B3
#21: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRV2
#22: Protein 30S ribosomal protein S15 /


Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A2J0WEG5
#23: Protein 30S ribosomal protein S16 /


Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XHU4
#24: Protein 30S ribosomal protein S17 /


Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A063XCK9
#25: Protein 30S ribosomal protein S18 /


Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A3A5I3T1
#26: Protein 30S ribosomal protein S19 /


Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: F5HRU0
#27: Protein 30S ribosomal protein S20 /


Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A086DNG8

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Protein , 1 types, 1 molecules z

#53: Protein Endonuclease MutS2


Mass: 87530.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mutS2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A857HL23

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Details

Has ligand of interestN

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1MutS2-disome complex from B. subtilis, focus refined, collided 70SRIBOSOMECollided ribosomes from B. subtilis (purified from natural source) reconstituted with recombinantly expressed and purified B. subtilis MutS2. Focus refined reconstruction, with a mask covering the collided ribosome and MutS2.#1-#6, #8-#28, #30-#52, #29, #53, #70MULTIPLE SOURCES
2B. subtilis Endonuclease MutS2 binding the collided ribosome interfaceCOMPLEX#531RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Bacillus subtilis (bacteria)1423
32Bacillus subtilis (bacteria)1423
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 43.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11794 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004155536
ELECTRON MICROSCOPYf_angle_d0.721232989
ELECTRON MICROSCOPYf_dihedral_angle_d16.75361823
ELECTRON MICROSCOPYf_chiral_restr0.03729811
ELECTRON MICROSCOPYf_plane_restr0.00612258

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  • 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

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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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