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- PDB-5tcu: Methicillin sensitive Staphylococcus aureus 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 5tcu
TitleMethicillin sensitive Staphylococcus aureus 70S ribosome
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 28
  • 16S RRNA
  • 23S RRNA23S ribosomal RNA
  • 5S rRNA CHAIN
  • E-site tRNA CHAIN
  • P-site tRNA CHAIN
  • mRNAMessenger RNA
Keywordsribosome/antibiotic / 70S ribosome / cryoEM / ribosome / Staphylococcus aureus / ribosome-antibiotic complex
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / 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 L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L31 type B / 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 L31 signature. / 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 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 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 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 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein S15, bacterial-type / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein S6 / Ribosomal protein S6
Similarity search - Domain/homology
PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 ...PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / 50S ribosomal protein L33 1 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15 / 30S ribosomal protein S10
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsEyal, Z. / Ahmed, T. / Belousoff, N. / Mishra, S. / Matzov, D. / Bashan, A. / Zimmerman, E. / Lithgow, T. / Bhushan, S. / Yonath, A.
Funding support Australia, European Union, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1092262 Australia
European Research Council (ERC)322581 (NOVRIB)European Union
CitationJournal: mBio / Year: 2017
Title: Structural Basis for Linezolid Binding Site Rearrangement in the Ribosome.
Authors: Matthew J Belousoff / Zohar Eyal / Mazdak Radjainia / Tofayel Ahmed / Rebecca S Bamert / Donna Matzov / Anat Bashan / Ella Zimmerman / Satabdi Mishra / David Cameron / Hans Elmlund / Anton Y ...Authors: Matthew J Belousoff / Zohar Eyal / Mazdak Radjainia / Tofayel Ahmed / Rebecca S Bamert / Donna Matzov / Anat Bashan / Ella Zimmerman / Satabdi Mishra / David Cameron / Hans Elmlund / Anton Y Peleg / Shashi Bhushan / Trevor Lithgow / Ada Yonath /
Abstract: An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of This high-resolution ...An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other
Category: atom_sites / cell ...atom_sites / cell / pdbx_audit_support / pdbx_struct_assembly / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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Assembly

Deposited unit
A: 16S RRNA
SB: 30S ribosomal protein S3
SC: 30S ribosomal protein S4
SD: 30S ribosomal protein S5
SE: 30S ribosomal protein S6
SG: 30S ribosomal protein S7
SF: 30S ribosomal protein S8
SH: 30S ribosomal protein S9
S1: 30S ribosomal protein S10
S2: 30S ribosomal protein S11
S3: 30S ribosomal protein S12
S4: 30S ribosomal protein S13
S5: 30S ribosomal protein S14 type Z
S6: 30S ribosomal protein S15
S7: 30S ribosomal protein S16
S8: 30S ribosomal protein S17
S9: 30S ribosomal protein S18
SI: 30S ribosomal protein S19
SA: 30S ribosomal protein S20
X: mRNA
E: P-site tRNA CHAIN
D: E-site tRNA CHAIN
B: 23S RRNA
C: 5S rRNA CHAIN
L2: 50S ribosomal protein L2
LC: 50S ribosomal protein L3
LJ: 50S ribosomal protein L4
LK: 50S ribosomal protein L5
LL: 50S ribosomal protein L6
LM: 50S ribosomal protein L13
LN: 50S ribosomal protein L14
LO: 50S ribosomal protein L15
LP: 50S ribosomal protein L16
LQ: 50S ribosomal protein L17
LR: 50S ribosomal protein L18
L1: 50S ribosomal protein L19
L3: 50S ribosomal protein L20
L4: 50S ribosomal protein L21
L5: 50S ribosomal protein L22
L6: 50S ribosomal protein L23
L7: 50S ribosomal protein L24
L8: 50S ribosomal protein L25
L9: 50S ribosomal protein L27
LA: 50S ribosomal protein L28
LB: 50S ribosomal protein L29
LD: 50S ribosomal protein L30
LE: 50S ribosomal protein L32
LS: 50S ribosomal protein L33 1
LG: 50S ribosomal protein L34
LH: 50S ribosomal protein L35
LI: 50S ribosomal protein L36
LF: 50S ribosomal protein L31 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,119,582182
Polymers2,115,83152
Non-polymers3,751130
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area234490 Å2
ΔGint-3026 kcal/mol
Surface area798640 Å2

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Components

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RNA chain , 6 types, 6 molecules AXEDBC

#1: RNA chain 16S RRNA /


Mass: 502935.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: GenBank: 87201381
#20: RNA chain mRNA / Messenger RNA


Mass: 4157.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ?
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
#21: RNA chain P-site tRNA CHAIN


Mass: 24156.334 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 1061489863
#22: RNA chain E-site tRNA CHAIN


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 1061489863
#23: RNA chain 23S RRNA / 23S ribosomal RNA


Mass: 946687.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: GenBank: 87201381
#24: RNA chain 5S rRNA CHAIN


Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: GenBank: 87201381

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30S ribosomal protein ... , 18 types, 18 molecules SBSCSDSESGSFSHS1S2S3S4S5S6S7S8S9SISA

#2: Protein 30S ribosomal protein S3 /


Mass: 22684.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW12
#3: Protein 30S ribosomal protein S4 /


Mass: 22849.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXK6
#4: Protein 30S ribosomal protein S5 /


Mass: 16522.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW23
#5: Protein 30S ribosomal protein S6 /


Mass: 11239.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G113
#6: Protein 30S ribosomal protein S7 /


Mass: 17695.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P48940
#7: Protein 30S ribosomal protein S8 /


Mass: 14622.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW20
#8: Protein 30S ribosomal protein S9 /


Mass: 14312.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW39
#9: Protein 30S ribosomal protein S10 /


Mass: 9243.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2YYP5
#10: Protein 30S ribosomal protein S11 /


Mass: 12047.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW31
#11: Protein 30S ribosomal protein S12 /


Mass: 15189.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0H0
#12: Protein 30S ribosomal protein S13 /


Mass: 12843.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW30
#13: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7186.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW19
#14: Protein 30S ribosomal protein S15 /


Mass: 10503.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G2Q1
#15: Protein 30S ribosomal protein S16 /


Mass: 9291.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ45
#16: Protein 30S ribosomal protein S17 /


Mass: 9366.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW15
#17: Protein 30S ribosomal protein S18 /


Mass: 6574.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G111
#18: Protein 30S ribosomal protein S19 /


Mass: 9010.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW10
#19: Protein 30S ribosomal protein S20 /


Mass: 8609.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXY6

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50S ribosomal protein ... , 28 types, 28 molecules L2LCLJLKLLLMLNLOLPLQLRL1L3L4L5L6L7L8L9LALBLDLELSLGLHLILF

#25: Protein 50S ribosomal protein L2 /


Mass: 29827.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P60430
#26: Protein 50S ribosomal protein L3 /


Mass: 23199.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW06
#27: Protein 50S ribosomal protein L4 /


Mass: 22293.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW07
#28: Protein 50S ribosomal protein L5 /


Mass: 18758.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW18
#29: Protein 50S ribosomal protein L6 /


Mass: 19400.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW21
#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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW38
#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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW16
#32: Protein 50S ribosomal protein L15 /


Mass: 15515.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0F8
#33: Protein 50S ribosomal protein L16 /


Mass: 15486.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW13
#34: Protein 50S ribosomal protein L17 /


Mass: 13420.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW33
#35: Protein 50S ribosomal protein L18 /


Mass: 12461.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW22
#36: Protein 50S ribosomal protein L19 /


Mass: 12463.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ42
#37: Protein 50S ribosomal protein L20 /


Mass: 13459.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXQ1
#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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXS8
#39: Protein 50S ribosomal protein L22 /


Mass: 12328.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW11
#40: Protein 50S ribosomal protein L23 /


Mass: 10380.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW08
#41: Protein 50S ribosomal protein L24 /


Mass: 11316.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW17
#42: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 10391.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2G0S0
#43: Protein 50S ribosomal protein L27 /


Mass: 8911.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXT0
#44: Protein 50S ribosomal protein L28 /


Mass: 6550.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FZ60
#45: Protein 50S ribosomal protein L29 /


Mass: 7331.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW14
#46: Protein 50S ribosomal protein L30 /


Mass: 6305.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: P0A0G2
#47: Protein/peptide 50S ribosomal protein L32 /


Mass: 5406.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: A7X145
#48: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 5684.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FYU6
#49: Protein/peptide 50S ribosomal protein L34 /


Mass: 5252.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FUQ0
#50: Protein 50S ribosomal protein L35 /


Mass: 6985.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FXQ0
#51: 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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FW29
#52: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 8603.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / References: UniProt: Q2FWD8

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Non-polymers , 2 types, 130 molecules

#53: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 129 / 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

ComponentName: Methicillin sensitive Staphylococcus aureus 70S ribosome (ATCC 35556)
Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.6
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: (dev_2429: phenix.real_space_refine) / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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