[English] 日本語
Yorodumi
- PDB-6fxc: The cryo-EM structure of hibernating 100S ribosome dimer from pat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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
Function / homology
Function and homology information


primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain ...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 / 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 S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS7 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS7 / 50S ribosomal protein L27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL25 / : / Small ribosomal subunit protein uS9 / 50S ribosomal protein L32 / Large ribosomal subunit protein bL27 / Ribosome hibernation promotion factor / 30S ribosomal protein S21 / 30S ribosomal protein S20 / 50S ribosomal protein L21 / 50S ribosomal protein L35 / 50S ribosomal protein L20 / 30S ribosomal protein S4 / 50S ribosomal protein L31 type B / 30S ribosomal protein S6 / 30S ribosomal protein S16 / 50S ribosomal protein L28 / 30S ribosomal protein S2 / 50S ribosomal protein L19 / 30S ribosomal protein S15 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 30S ribosomal protein S13 / 30S ribosomal protein S11 / 50S ribosomal protein L17 / 50S ribosomal protein L13 / 50S ribosomal protein L29 / 30S ribosomal protein S10 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 30S ribosomal protein S3 / 50S ribosomal protein L16 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.76 Å
AuthorsMatzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Kidmose, R. / Amunts, A. / Yonath, A.
Funding support Sweden, Israel, 2items
OrganizationGrant numberCountry
Swedish Research CouncilFFL15-0325 Sweden
European Research Council322581 Israel
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 8, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMar 21, 2018ID: 5NG8
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Structure summary
Category: entity / pdbx_database_related
Item: _entity.pdbx_description / _pdbx_database_related.content_type
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3637
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Polymers4,236,804104
Non-polymers00
Water0
1


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

-
Components

-
RNA chain , 3 types, 6 molecules AaBaAABAABBB

#1: RNA chain 16S ribosomal RNA /


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


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


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

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

#2: Protein 30S ribosomal protein S2 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

-
Protein , 1 types, 2 molecules AvBv

#22: Protein Ribosome hibernation promotion factor / HPF


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

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

#25: Protein 50S ribosomal protein L2 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 8911.099 Da / Num. of mol.: 2 / 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: 6550.716 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXJ2
#45: Protein 50S ribosomal protein L29 /


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


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


Mass: 6909.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source
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 method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q8DAT0
#49: Protein/peptide 50S ribosomal protein L33 /


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


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


Mass: 7461.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source
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 method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1100S complex pf Staphylococcus aureusRIBOSOMEall0NATURAL
230S subunitProkaryotic small ribosomal subunitCOMPLEX#1-#211NATURAL
350S subunitProkaryotic large ribosomal subunitCOMPLEX#23-#521NATURAL
416S rRNACOMPLEX#12NATURAL
530S ribosomal proteinsRibosomal proteinCOMPLEX#2-#212NATURAL
623S and 5S rRNACOMPLEX#23-#243NATURAL
750S ribosomal proteinsRibosomal proteinCOMPLEX#25-#523NATURAL
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

-
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)

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more