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- PDB-5nd8: Hibernating ribosome from Staphylococcus aureus (Unrotated state) -

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Basic information

Entry
Database: PDB / ID: 5nd8
TitleHibernating ribosome from Staphylococcus aureus (Unrotated state)
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 / S.aureus / HPF / hibernation / 100S ribosome
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
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 / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L31 type B / 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 / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 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 S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / 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 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL33B / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Ribosome hibernation promotion factor / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKhusainov, I. / Vicens, Q. / Ayupov, R. / Usachev, K. / Myasnikov, A. / Simonetti, A. / Validov, S. / Kieffer, B. / Yusupova, G. / Yusupov, M. / Hashem, Y.
Funding support France, Russian Federation, 5items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheANR-10-LABX-0036_NETRNA France
Centre National de la Recherche Scientifique and Agence Nationale de la RechercheANR-15-CE11-0021-01 France
Russian Science Foundation16-14-10014 Russian Federation
European Research Council294312
French National Research AgencyFDT20140930867 France
CitationJournal: EMBO J / Year: 2017
Title: Structures and dynamics of hibernating ribosomes from mediated by intermolecular interactions of HPF.
Authors: Iskander Khusainov / Quentin Vicens / Rustam Ayupov / Konstantin Usachev / Alexander Myasnikov / Angelita Simonetti / Shamil Validov / Bruno Kieffer / Gulnara Yusupova / Marat Yusupov / Yaser Hashem /
Abstract: In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of ...In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials.
History
DepositionMar 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Other / Category: cell / citation
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Feb 20, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: em_admin / pdbx_audit_support ...em_admin / pdbx_audit_support / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_audit_support.funding_organization ..._em_admin.last_update / _pdbx_audit_support.funding_organization / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.5Nov 6, 2019Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.6Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.7May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14 type Z
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: Ribosome hibernation promotion factor
A: 23S ribosomal RNA
B: 5S ribosomal RNA
D: 50S ribosomal protein L2
E: 50S ribosomal protein L3
F: 50S ribosomal protein L4
G: 50S ribosomal protein L5
H: 50S ribosomal protein L6
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Y: 50S ribosomal protein L25
Z: 50S ribosomal protein L27
0: 50S ribosomal protein L28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: 50S ribosomal protein L31 type B
4: 50S ribosomal protein L32
5: 50S ribosomal protein L33 2
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36


Theoretical massNumber of molelcules
Total (without water)2,160,70452
Polymers2,160,70452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230980 Å2
ΔGint-1894 kcal/mol
Surface area791170 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules aAB

#1: RNA chain 16S ribosomal RNA


Mass: 500464.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381
#23: RNA chain 23S ribosomal RNA


Mass: 945058.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381
#24: RNA chain 5S ribosomal RNA


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

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

#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ25
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW12
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXK6
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW23
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2G113
#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 (strain NCTC 8325) (bacteria)
References: UniProt: P48940
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW20
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW39
#10: Protein 30S ribosomal protein S10


Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: A7X5G6
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW31
#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 (strain NCTC 8325) (bacteria)
References: UniProt: P0A0H0
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW30
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW19
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2G2Q1
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ45
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW15
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2G111
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW10
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXY6
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXZ7

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Protein , 1 types, 1 molecules v

#22: Protein Ribosome hibernation promotion factor / HPF / Hibernation promoting factor SaHPF


Mass: 22244.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Gene: hpf, SAOUHSC_00767 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2G055

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50S ribosomal protein ... , 28 types, 28 molecules DEFGHMNOPQRSTUVWXYZ012345678

#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 (strain NCTC 8325) (bacteria)
References: UniProt: P60430
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW06
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW07
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW18
#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 (strain NCTC 8325) (bacteria)
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)
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)
References: UniProt: Q2FW16
#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 (strain NCTC 8325) (bacteria)
References: UniProt: P0A0F8
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW13
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW33
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW22
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ42
#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 (strain NCTC 8325) (bacteria)
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)
References: UniProt: Q2FXS8
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW11
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW08
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW17
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2G0S0
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXT0
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZ60
#45: Protein 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW14
#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 (strain NCTC 8325) (bacteria)
References: UniProt: P0A0G2
#47: Protein 50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FWD8
#48: Protein 50S ribosomal protein L32


Mass: 6657.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FZF1
#49: Protein/peptide 50S ribosomal protein L33 2


Mass: 5885.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria)
References: UniProt: Q2FY22
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FUQ0
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FXQ0
#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 (strain NCTC 8325) (bacteria)
References: UniProt: Q2FW29

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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
IDNameTypeDetailsEntity IDParent-IDSource
1Hibernating ribosome from Staphylococcus aureus (Unrotated state)RIBOSOME70S monosome derived from 100S disomeall0MULTIPLE SOURCES
2Hibernating ribosome from Staphylococcus aureus (Unrotated state)RIBOSOME70S monosome derived from 100S disome#1-#21, #23-#521NATURAL
3Ribosome hibernation promotion factorRIBOSOME70S monosome derived from 100S disome#221RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Staphylococcus aureus (strain NCTC 8325) (bacteria)93061
23Staphylococcus aureus (strain NCTC 8325) (bacteria)93061
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
Details: 5 mM Hepes-KOH pH 7.5 50 mM KCl 10 mM NH4Cl 10 mM Mg(OAc)2 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5, blot waiting time 30 s

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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: DARK FIELD
Image recordingAverage exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 17 / Used frames/image: 2-8

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Processing

SoftwareName: PHENIX / Version: 1.11_2567: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIX1.10.1-2155model fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
12RELION1.33D reconstruction
13PHENIX1.10.1-2155model refinement
14ERRASER1.10.1-2155model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 348000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011247472
ELECTRON MICROSCOPYf_angle_d1.296444911
ELECTRON MICROSCOPYf_dihedral_angle_d23.32296432
ELECTRON MICROSCOPYf_chiral_restr0.06329382
ELECTRON MICROSCOPYf_plane_restr0.00621325

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