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- PDB-5ngm: 2.9S structure of the 70S ribosome composing the S. aureus 100S c... -

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Entry
Database: PDB / ID: 5ngm
Title2.9S structure of the 70S ribosome composing the S. aureus 100S complex
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / Ribosome Cryo-EM Structural Biology Hibernation
Function / homology
Function and homology information


primary metabolic process / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...primary metabolic process / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
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 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Type-1 KH domain profile. / Ribosomal protein L25, long-form ...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 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Type-1 KH domain profile. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / 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 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 / Ribosomal protein L27
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S21 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18 / 30S ribosomal protein S19 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS10 / 50S ribosomal protein L29 / 30S ribosomal protein S9 / 50S ribosomal protein L27 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL27 / Ribosome hibernation promoting factor / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / 50S ribosomal protein L31 type B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS13 / Ribosome hibernation promoting factor / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein bS20
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMatzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Amunts, A. / Yonath, A.
CitationJournal: Nat Commun / Year: 2017
Title: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Authors: Donna Matzov / Shintaro Aibara / Arnab Basu / Ella Zimmerman / Anat Bashan / Mee-Ngan F Yap / Alexey Amunts / Ada E Yonath /
Abstract: Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were ...Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors.
History
DepositionMar 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

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Assembly

Deposited unit
Aa: 16S ribosomal RNA
Ab: 30S ribosomal protein S2
Ac: 30S ribosomal protein S3
Ad: 30S ribosomal protein S4
Ae: 30S ribosomal protein S5
Af: 30S ribosomal protein S6
Ag: 30S ribosomal protein S7
Ah: 30S ribosomal protein S8
Ai: 30S ribosomal protein S9
Aj: 30S ribosomal protein S10
Ak: 30S ribosomal protein S11
Al: 30S ribosomal protein S12
Am: 30S ribosomal protein S13
An: 30S ribosomal protein S14 type Z
Ao: 30S ribosomal protein S15
Ap: 30S ribosomal protein S16
Aq: 30S ribosomal protein S17
Ar: 30S ribosomal protein S18
As: 30S ribosomal protein S19
At: 30S ribosomal protein S20
Au: 30S ribosomal protein S21
Av: Ribosome hibernation promoting factor
AA: 23S Ribosomal RNA
AB: 5S Ribosomal RNA
AC: 50S ribosomal protein L2
AD: 50S ribosomal protein L3
AE: 50S ribosomal protein L4
AF: 50S ribosomal protein L5
AG: 50S ribosomal protein L6
AH: 50S ribosomal protein L13
AI: 50S ribosomal protein L14
AJ: 50S ribosomal protein L15
AK: 50S ribosomal protein L16
AL: 50S ribosomal protein L17
AM: 50S ribosomal protein L18
AN: 50S ribosomal protein L19
AO: 50S ribosomal protein L20
AP: 50S ribosomal protein L21
AQ: 50S ribosomal protein L22
AR: 50S ribosomal protein L23
AS: 50S ribosomal protein L24
AT: 50S ribosomal protein L25
AU: 50S ribosomal protein L27
AV: 50S ribosomal protein L28
AW: 50S ribosomal protein L29
AX: 50S ribosomal protein L30
AY: 50S ribosomal protein L31 type B
AZ: 50S ribosomal protein L32
A1: 50S ribosomal protein L33
A2: 50S ribosomal protein L34
A3: 50S ribosomal protein L35
A4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,170,506257
Polymers2,165,52452
Non-polymers4,983205
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules AaAAAB

#1: RNA chain 16S ribosomal RNA /


Mass: 502975.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1133392934
#23: RNA chain 23S Ribosomal RNA /


Mass: 946697.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 610395799
#24: RNA chain 5S Ribosomal RNA /


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1130374198

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30S ribosomal protein ... , 20 types, 20 molecules AbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAu

#2: Protein 30S ribosomal protein S2 /


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UDU1
#3: Protein 30S ribosomal protein S3 /


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UU26
#4: Protein 30S ribosomal protein S4 /


Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TVK2
#5: Protein 30S ribosomal protein S5 /


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC9
#6: Protein 30S ribosomal protein S6 /


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TPC6
#7: Protein 30S ribosomal protein S7 /


Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VHU6
#8: Protein 30S ribosomal protein S8 /


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8T8
#9: Protein 30S ribosomal protein S9 /


Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0K7UQP6
#10: Protein 30S ribosomal protein S10 /


Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H2K0A0
#11: Protein 30S ribosomal protein S11 /


Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKD6
#12: Protein 30S ribosomal protein S12 /


Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U1C6
#13: Protein 30S ribosomal protein S13 /


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U8U6
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGW7
#15: Protein 30S ribosomal protein S15 /


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6H8
#16: Protein 30S ribosomal protein S16 /


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U6K4
#17: Protein 30S ribosomal protein S17 /


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VLD5
#18: Protein 30S ribosomal protein S18 /


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UZF4
#19: Protein 30S ribosomal protein S19 /


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V0P8
#20: Protein 30S ribosomal protein S20 /


Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UXC3
#21: Protein 30S ribosomal protein S21 /


Mass: 6994.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UHS1

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50S ribosomal protein ... , 28 types, 28 molecules ACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZA1A2A3A4

#25: Protein 50S ribosomal protein L2 /


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077W1J0
#26: Protein 50S ribosomal protein L3 /


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3W0
#27: Protein 50S ribosomal protein L4 /


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRC7
#28: Protein 50S ribosomal protein L5 /


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUC3
#29: Protein 50S ribosomal protein L6 /


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3X2
#30: Protein 50S ribosomal protein L13 /


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUE6
#31: Protein 50S ribosomal protein L14 /


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UUA0
#32: Protein 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGA7
#33: Protein 50S ribosomal protein L16 /


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V4G0
#34: Protein 50S ribosomal protein L17 /


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UG91
#35: Protein 50S ribosomal protein L18 /


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0
#36: Protein 50S ribosomal protein L19 /


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UVB6
#37: Protein 50S ribosomal protein L20 /


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VMP6
#38: Protein 50S ribosomal protein L21 /


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: D7URR3
#39: Protein 50S ribosomal protein L22 /


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKF9
#40: Protein 50S ribosomal protein L23 /


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUB4
#41: Protein 50S ribosomal protein L24 /


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRD5
#42: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133Q8Z9
#43: Protein 50S ribosomal protein L27 /


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0U1N012, UniProt: A0A7U7PYN3*PLUS
#44: Protein 50S ribosomal protein L28 /


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077URJ8
#45: Protein 50S ribosomal protein L29 /


Mass: 8592.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0H3KED7
#46: Protein 50S ribosomal protein L30 /


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UVN7
#47: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRP5
#48: Protein 50S ribosomal protein L32 /


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UWR7
#49: Protein/peptide 50S ribosomal protein L33 /


Mass: 5944.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V2P0
#50: Protein/peptide 50S ribosomal protein L34 /


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YZB6
#51: Protein 50S ribosomal protein L35 /


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UL47
#52: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8

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Protein / Non-polymers , 2 types, 206 molecules Av

#22: Protein Ribosome hibernation promoting factor / HPF


Mass: 22244.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8USK0, UniProt: D2Z097*PLUS
#53: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 205 / Source method: obtained synthetically / Formula: Mg

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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
IDNameTypeEntity IDParent-IDSource
170S ribosome of the S. aureus 100S complexRIBOSOME#1-#520NATURAL
230S subunitProkaryotic small ribosomal subunitCOMPLEX#1-#221NATURAL
316S rRNACOMPLEX#12NATURAL
430S ribosomal proteinsRibosomal proteinCOMPLEX#2-#212NATURAL
550S subunitProkaryotic large ribosomal subunitCOMPLEX#23-#521NATURAL
623S and 5S rRNACOMPLEX#23-#245NATURAL
750S ribosomal proteinsRibosomal proteinCOMPLEX#25-#525NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
12
13
14
15
16
17
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Staphylococcus aureus (bacteria)1280USA300_FPR3757
32Staphylococcus aureus (bacteria)1280USA300_FPR3757
43Staphylococcus aureus (bacteria)1280USA300_FPR3757
54Staphylococcus aureus (bacteria)1280USA300_FPR3757
65Staphylococcus aureus (bacteria)1280USA300_FPR3757
76Staphylococcus aureus (bacteria)1280USA300_FPR3757
87Staphylococcus aureus (bacteria)1280USA300_FPR3757
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
Image recordingElectron dose: 2.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224554 / Symmetry type: POINT

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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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