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- PDB-3j9w: Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome ... -

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Basic information

Entry
Database: PDB / ID: 3j9w
TitleCryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • MifM
  • mRNAMessenger RNA
  • tRNA-Asp
KeywordsRIBOSOME / stalling / translation arrest / mifm / L22
Function / homology
Function and homology information


positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit ...positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / membrane => GO:0016020 / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / 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 L10, eubacterial, conserved site / Ribosomal protein L10 signature. / 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 L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L10 / Ribosomal protein L10P / 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 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, RNA binding domain / Ribosomal protein L11/L12 / 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 S14/S29 / 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 L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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 L20 / Ribosomal protein L20, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein L21
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / 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 uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL11 / Membrane protein insertion and folding monitor
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSohmen, D. / Chiba, S. / Shimokawa-Chiba, N. / Innis, C.A. / Berninghausen, O. / Beckmann, R. / Ito, K. / Wilson, D.N.
CitationJournal: Nat Commun / Year: 2015
Title: Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Authors: Daniel Sohmen / Shinobu Chiba / Naomi Shimokawa-Chiba / C Axel Innis / Otto Berninghausen / Roland Beckmann / Koreaki Ito / Daniel N Wilson /
Abstract: Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream ...Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5-3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-6306
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Structure viewerMolecule:
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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein uS2
AC: 30S ribosomal protein uS3
AD: 30S ribosomal protein uS4
AE: 30S ribosomal protein uS5
AF: 30S ribosomal protein bS6
AG: 30S ribosomal protein uS7
AH: 30S ribosomal protein uS8
AI: 30S ribosomal protein uS9
AJ: 30S ribosomal protein uS10
AK: 30S ribosomal protein uS11
AL: 30S ribosomal protein uS12
AM: 30S ribosomal protein uS13
AN: 30S ribosomal protein uS14
AO: 30S ribosomal protein uS15
AP: 30S ribosomal protein bS16
AQ: 30S ribosomal protein uS17
AR: 30S ribosomal protein bS18
AS: 30S ribosomal protein uS19
AT: 30S ribosomal protein bS20
AX: tRNA-Asp
AY: mRNA
AZ: MifM
B0: 50S ribosomal protein bL28
B1: 50S ribosomal protein uL29
B2: 50S ribosomal protein uL30
B3: 50S ribosomal protein bL31
B4: 50S ribosomal protein bL32
B5: 50S ribosomal protein bL33
B6: 50S ribosomal protein bL34
B7: 50S ribosomal protein bL35
B8: 50S ribosomal protein bL36
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein uL2
BE: 50S ribosomal protein uL3
BF: 50S ribosomal protein uL4
BG: 50S ribosomal protein uL5
BH: 50S ribosomal protein uL6
BJ: 50S ribosomal protein uL10
BK: 50S ribosomal protein uL11
BM: 50S ribosomal protein uL13
BN: 50S ribosomal protein uL14
BO: 50S ribosomal protein uL15
BP: 50S ribosomal protein uL16
BQ: 50S ribosomal protein bL17
BR: 50S ribosomal protein uL18
BS: 50S ribosomal protein bL19
BT: 50S ribosomal protein bL20
BU: 50S ribosomal protein bL21
BV: 50S ribosomal protein uL22
BW: 50S ribosomal protein uL23
BX: 50S ribosomal protein uL24
BZ: 50S ribosomal protein bL27


Theoretical massNumber of molelcules
Total (without water)2,185,39954
Polymers2,185,39954
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules AAAXAYBABB

#1: RNA chain 16S ribosomal RNA /


Mass: 503698.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#21: RNA chain tRNA-Asp


Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#22: RNA chain mRNA / Messenger RNA


Mass: 6204.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#33: RNA chain 23S ribosomal RNA /


Mass: 949606.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#34: RNA chain 5S ribosomal RNA /


Mass: 38423.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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

#2: Protein 30S ribosomal protein uS2 /


Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21464
#3: Protein 30S ribosomal protein uS3 /


Mass: 24364.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#4: Protein 30S ribosomal protein uS4 /


Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21466
#5: Protein 30S ribosomal protein uS5 /


Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#6: Protein 30S ribosomal protein bS6 /


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468
#7: Protein 30S ribosomal protein uS7 /


Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469
#8: Protein 30S ribosomal protein uS8 /


Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#9: Protein 30S ribosomal protein uS9 /


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#10: Protein 30S ribosomal protein uS10 /


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#11: Protein 30S ribosomal protein uS11 /


Mass: 13952.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#12: Protein 30S ribosomal protein uS12 /


Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#13: Protein 30S ribosomal protein uS13 /


Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#14: Protein 30S ribosomal protein uS14 /


Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#15: Protein 30S ribosomal protein uS15 /


Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#16: Protein 30S ribosomal protein bS16 /


Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21474
#17: Protein 30S ribosomal protein uS17 /


Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#18: Protein 30S ribosomal protein bS18 /


Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#19: Protein 30S ribosomal protein uS19 /


Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#20: Protein 30S ribosomal protein bS20 /


Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477

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Protein , 1 types, 1 molecules AZ

#23: Protein MifM


Mass: 11156.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q7WY64

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50S ribosomal protein ... , 29 types, 29 molecules B0B1B2B3B4B5B6B7B8BDBEBFBGBHBJBKBMBNBOBPBQBRBSBTBUBVBWBXBZ

#24: Protein 50S ribosomal protein bL28 /


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#25: Protein 50S ribosomal protein uL29 /


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#26: Protein 50S ribosomal protein uL30 /


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#27: Protein 50S ribosomal protein bL31 /


Mass: 7458.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223
#28: Protein 50S ribosomal protein bL32 /


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#29: Protein/peptide 50S ribosomal protein bL33 /


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#30: Protein/peptide 50S ribosomal protein bL34 /


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#31: Protein 50S ribosomal protein bL35 /


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#32: Protein/peptide 50S ribosomal protein bL36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#35: Protein 50S ribosomal protein uL2 /


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#36: Protein 50S ribosomal protein uL3 /


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#37: Protein 50S ribosomal protein uL4 /


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#38: Protein 50S ribosomal protein uL5 /


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#39: Protein 50S ribosomal protein uL6 /


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#40: Protein 50S ribosomal protein uL10 /


Mass: 18101.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42923
#41: Protein 50S ribosomal protein uL11 /


Mass: 14951.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q06796
#42: Protein 50S ribosomal protein uL13 /


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#43: Protein 50S ribosomal protein uL14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#44: Protein 50S ribosomal protein uL15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#45: Protein 50S ribosomal protein uL16 /


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#46: Protein 50S ribosomal protein bL17 /


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#47: Protein 50S ribosomal protein uL18 /


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#48: Protein 50S ribosomal protein bL19 /


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#49: Protein 50S ribosomal protein bL20 /


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#50: Protein 50S ribosomal protein bL21 /


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#51: Protein 50S ribosomal protein uL22 /


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#52: Protein 50S ribosomal protein uL23 /


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#53: Protein 50S ribosomal protein uL24 /


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#54: Protein 50S ribosomal protein bL27 /


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657

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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
IDNameTypeParent-ID
1B. subtilis MifM-stalled ribosome complexRIBOSOME0
270S ribosomeRibosomeRIBOSOME1
3Membrane protein insertion and folding monitorBiological membrane1
4tRNA-Asp1
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 2 nm pre-coated Quantifoil R3/3 holey carbon support grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 125085 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305045 / Nominal pixel size: 1.108 Å / Actual pixel size: 1.108 Å
Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A ...Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms35090 100335 0 0 135425

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