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- PDB-6fxc: The cryo-EM structure of hibernating 100S ribosome dimer from pat... -

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Entry
Database: PDB / ID: 6fxc
TitleThe cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome hibernation promotion factor
KeywordsRIBOSOME / Ribosome Cryo-EM Structural Biology Hibernation / ribosome
Function / homologyRibosomal protein L17 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily ...Ribosomal protein L17 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein S21 superfamily / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Ribosomal protein L19 superfamily / Ribosome hibernation promotion factor-like / Ribosomal protein L16p/L10e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L14p/L23e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein L21-like / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, type Z / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type B / Ribosomal protein L25 / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S2 signature 2. / Ribosomal L18e/L15P superfamily / L21-like superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L15 / Ribosomal protein L20, C-terminal / L28p-like / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L30p/L7e / Ribosomal protein S10p/S20e / Ribosomal protein L2, C-terminal / Ribosomal protein L22 signature. / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L14 signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein L5 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein L2 signature. / KH domain / Ribosomal protein S4 signature. / Ribosomal protein L35 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature. / Ribosomal protein L13 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein S13 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L3 signature. / Ribosomal protein S5 signature. / Ribosomal protein L33 signature. / Ribosomal protein S3 signature.
Function and homology information
Specimen sourceStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.76 Å resolution
AuthorsMatzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Kidmose, R. / 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 8, 2018 / Release: Mar 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 21, 2018Structure modelrepositoryInitial release
1.1May 30, 2018Structure modelData collection / Database references / Structure summaryentity / pdbx_database_related_entity.pdbx_description / _pdbx_database_related.content_type
1.2Nov 21, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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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 promotion 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
Ba: 16S ribosomal RNA
Bb: 30S ribosomal protein S2
Bc: 30S ribosomal protein S3
Bd: 30S ribosomal protein S4
Be: 30S ribosomal protein S5
Bf: 30S ribosomal protein S6
Bg: 30S ribosomal protein S7
Bh: 30S ribosomal protein S8
Bi: 30S ribosomal protein S9
Bj: 30S ribosomal protein S10
Bk: 30S ribosomal protein S11
Bl: 30S ribosomal protein S12
Bm: 30S ribosomal protein S13
Bn: 30S ribosomal protein S14 type Z
Bo: 30S ribosomal protein S15
Bp: 30S ribosomal protein S16
Bq: 30S ribosomal protein S17
Br: 30S ribosomal protein S18
Bs: 30S ribosomal protein S19
Bt: 30S ribosomal protein S20
Bu: 30S ribosomal protein S21
Bv: Ribosome hibernation promotion factor
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L13
BI: 50S ribosomal protein L14
BJ: 50S ribosomal protein L15
BK: 50S ribosomal protein L16
BL: 50S ribosomal protein L17
BM: 50S ribosomal protein L18
BN: 50S ribosomal protein L19
BO: 50S ribosomal protein L20
BP: 50S ribosomal protein L21
BQ: 50S ribosomal protein L22
BR: 50S ribosomal protein L23
BS: 50S ribosomal protein L24
BT: 50S ribosomal protein L25
BU: 50S ribosomal protein L27
BV: 50S ribosomal protein L28
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
BY: 50S ribosomal protein L31 type B
BZ: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36


Theoretical massNumber of molelcules
Total (without water)4,236,804104
Polyers4,236,804104
Non-polymers00
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, 6 molecules AaBaAABAABBB

#1: RNA chain 16S ribosomal RNA /


Mass: 498060.031 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1248686583
#23: RNA chain 23S ribosomal RNA /


Mass: 946697.625 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 743649775
#24: RNA chain 5S ribosomal RNA /


Mass: 36974.945 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1269120188

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30S ribosomal protein ... , 20 types, 40 molecules AbBbAcBcAdBdAeBeAfBfAgBgAhBhAiBiAjBjAkBkAlBlAmBmAnBnAoBoApBp...

#2: Protein/peptide 30S ribosomal protein S2 /


Mass: 25929.135 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXL2
#3: Protein/peptide 30S ribosomal protein S3 /


Mass: 22684.201 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYQ2
#4: Protein/peptide 30S ribosomal protein S4 /


Mass: 22849.145 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YTH0
#5: Protein/peptide 30S ribosomal protein S5 /


Mass: 16522.119 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL4
#6: Protein/peptide 30S ribosomal protein S6 /


Mass: 11239.766 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YVJ2
#7: Protein/peptide 30S ribosomal protein S7 /


Mass: 17181.830 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VHU6
#8: Protein/peptide 30S ribosomal protein S8 /


Mass: 14723.118 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL1
#9: Protein/peptide 30S ribosomal protein S9 /


Mass: 14312.321 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q4GY48
#10: Protein/peptide 30S ribosomal protein S10 /


Mass: 11009.742 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP5
#11: Protein/peptide 30S ribosomal protein S11 /


Mass: 12047.609 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM1
#12: Protein/peptide 30S ribosomal protein S12 /


Mass: 15075.570 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PZQ5
#13: Protein/peptide 30S ribosomal protein S13 /


Mass: 13747.919 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM0
#14: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7186.573 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL0
#15: Protein/peptide 30S ribosomal protein S15 /


Mass: 10503.135 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXP3
#16: Protein/peptide 30S ribosomal protein S16 /


Mass: 9993.510 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXH8
#17: Protein/peptide 30S ribosomal protein S17 /


Mass: 9366.860 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYK6
#18: Protein/peptide 30S ribosomal protein S18 /


Mass: 6404.623 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1D4K9U8
#19: Protein/peptide 30S ribosomal protein S19 /


Mass: 9205.604 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PYC3
#20: Protein/peptide 30S ribosomal protein S20 /


Mass: 8779.096 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YT41
#21: Protein/peptide 30S ribosomal protein S21 /


Mass: 6241.280 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YT04

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Protein/peptide , 1 types, 2 molecules AvBv

#22: Protein/peptide Ribosome hibernation promotion factor / HPF


Mass: 22244.914 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YSH7

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50S ribosomal protein ... , 28 types, 56 molecules ACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBPAQBQ...

#25: Protein/peptide 50S ribosomal protein L2 /


Mass: 29827.607 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP9
#26: Protein/peptide 50S ribosomal protein L3 /


Mass: 23199.545 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP6
#27: Protein/peptide 50S ribosomal protein L4 /


Mass: 22364.504 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP7
#28: Protein/peptide 50S ribosomal protein L5 /


Mass: 19731.893 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYK9
#29: Protein/peptide 50S ribosomal protein L6 /


Mass: 19501.154 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL2
#30: Protein/peptide 50S ribosomal protein L13 /


Mass: 16359.427 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM8
#31: Protein/peptide 50S ribosomal protein L14 /


Mass: 13157.342 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYK7
#32: Protein/peptide 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL6
#33: Protein/peptide 50S ribosomal protein L16 /


Mass: 15599.435 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYQ3
#34: Protein/peptide 50S ribosomal protein L17 /


Mass: 13583.523 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM3
#35: Protein/peptide 50S ribosomal protein L18 /


Mass: 13124.093 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0
#36: Protein/peptide 50S ribosomal protein L19 /


Mass: 13104.381 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXM4
#37: Protein/peptide 50S ribosomal protein L20 /


Mass: 13459.919 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YTB1
#38: Protein/peptide 50S ribosomal protein L21 /


Mass: 11354.081 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YT83
#39: Protein/peptide 50S ribosomal protein L22 /


Mass: 12328.358 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYQ1
#40: Protein/peptide 50S ribosomal protein L23 /


Mass: 10380.100 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP8
#41: Protein/peptide 50S ribosomal protein L24 /


Mass: 11316.205 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYK8
#42: Protein/peptide 50S ribosomal protein L25 / / General stress protein CTC


Mass: 10462.200 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133Q8Z9
#43: Protein/peptide 50S ribosomal protein L27 /


Mass: 8911.099 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A0U1N012
#44: Protein/peptide 50S ribosomal protein L28 /


Mass: 6550.716 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXJ2
#45: Protein/peptide 50S ribosomal protein L29 /


Mass: 7845.942 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYN0
#46: Protein/peptide 50S ribosomal protein L30 /


Mass: 6434.487 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL5
#47: Protein/peptide 50S ribosomal protein L31 type B / Ribosome


Mass: 6909.694 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YUN3
#48: Protein/peptide 50S ribosomal protein L32 /


Mass: 5569.565 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q8DAT0
#49: Protein/peptide 50S ribosomal protein L33 /


Mass: 5684.561 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V2P0
#50: Protein/peptide 50S ribosomal protein L34 /


Mass: 5252.369 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YZB6
#51: Protein/peptide 50S ribosomal protein L35 /


Mass: 7461.992 Da / Num. of mol.: 2
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YTB0
#52: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 2 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1100S complex pf Staphylococcus aureusRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 520NATURAL
230S subunitCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 211NATURAL
350S subunitCOMPLEX23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 521NATURAL
416S rRNACOMPLEX12NATURAL
530S ribosomal proteinsCOMPLEX2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 212NATURAL
623S and 5S rRNACOMPLEX23, 243NATURAL
750S ribosomal proteinsCOMPLEX25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 523NATURAL
Molecular weight
IDEntity assembly IDExperimental value
11NO
12
13
14
15
16
17
Source (natural)
IDEntity assembly IDNcbi tax IDOrganismStrain
211280Staphylococcus aureus (bacteria)USA300_FPR3757
321280Staphylococcus aureus (bacteria)USA300_FPR3757
431280Staphylococcus aureus (bacteria)USA300_FPR3757
541280Staphylococcus aureus (bacteria)USA300_FPR3757
651280Staphylococcus aureus (bacteria)USA300_FPR3757
761280Staphylococcus aureus (bacteria)USA300_FPR3757
871280Staphylococcus aureus (bacteria)USA300_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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.3 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 6.76 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12570 / Number of class averages: 1 / Symmetry type: POINT

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Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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.

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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