[English] 日本語
Yorodumi
- PDB-7n1p: Elongating 70S ribosome complex in a classical pre-translocation ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n1p
TitleElongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • (tRNA) x 2
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Chains: Pp
  • mRNA
KeywordsRIBOSOME / Elongation complex / tRNA / mRNA
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / large ribosomal subunit / regulation of translation / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / : / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / 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 S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / 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 L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S12 ...ADENOSINE-5'-TRIPHOSPHATE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsRundlet, E.J. / Holm, M. / Schacherl, M. / Natchiar, S.K. / Altman, R.B. / Spahn, C.M.T. / Myasnikov, A.G. / Blanchard, S.C.
CitationJournal: Nature / Year: 2021
Title: Structural basis of early translocation events on the ribosome.
Authors: Emily J Rundlet / Mikael Holm / Magdalena Schacherl / S Kundhavai Natchiar / Roger B Altman / Christian M T Spahn / Alexander G Myasnikov / Scott C Blanchard /
Abstract: Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around ...Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10 to 10 at each step) over thousands of cycles. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 14, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 19, 2025Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Mar 19, 2025Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _em_admin.last_update
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-24120
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
16: 16S rRNA
SB: 30S ribosomal protein S2
SC: 30S ribosomal protein S3
SD: 30S ribosomal protein S4
SE: 30S ribosomal protein S5
SF: 30S ribosomal protein S6
SG: 30S ribosomal protein S7
SH: 30S ribosomal protein S8
SI: 30S ribosomal protein S9
SJ: 30S ribosomal protein S10
SK: 30S ribosomal protein S11
SL: 30S ribosomal protein S12
SM: 30S ribosomal protein S13
SN: 30S ribosomal protein S14
SO: 30S ribosomal protein S15
SP: 30S ribosomal protein S16
SQ: 30S ribosomal protein S17
SR: 30S ribosomal protein S18
SS: 30S ribosomal protein S19
ST: 30S ribosomal protein S20
SU: 30S ribosomal protein S21
mR: mRNA
23: 23S rRNA
5: 5S rRNA
LB: 50S ribosomal protein L2
LC: 50S ribosomal protein L3
LD: 50S ribosomal protein L4
LE: 50S ribosomal protein L5
LF: 50S ribosomal protein L6
LI: 50S ribosomal protein L9
LJ: 50S ribosomal protein L10
LK: 50S ribosomal protein L11
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
LS: 50S ribosomal protein L19
LT: 50S ribosomal protein L20
LU: 50S ribosomal protein L21
LV: 50S ribosomal protein L22
LW: 50S ribosomal protein L23
LX: 50S ribosomal protein L24
LY: 50S ribosomal protein L25
La: 50S ribosomal protein L27
Lb: 50S ribosomal protein L28
Lc: 50S ribosomal protein L29
Ld: 50S ribosomal protein L30
Le: 50S ribosomal protein L31
Lf: 50S ribosomal protein L32
Lg: 50S ribosomal protein L33
Lh: 50S ribosomal protein L34
Li: 50S ribosomal protein L35
Lj: 50S ribosomal protein L36
Pt: tRNA
Pp: Chains: Pp
Dt: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,255,982492
Polymers2,242,10858
Non-polymers13,874434
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 6 types, 6 molecules 16mR235PtDt

#1: RNA chain 16S rRNA


Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: GenBank: 1789840096
#22: RNA chain mRNA


Mass: 19128.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli BL21 (bacteria)
#23: RNA chain 23S rRNA


Mass: 941795.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600
#24: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600 / References: GenBank: 991970073
#56: RNA chain tRNA


Mass: 24703.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNA / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MRE600 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MRE600
#58: RNA chain tRNA


Mass: 24733.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MRE600 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MRE600

-
30S ribosomal protein ... , 20 types, 20 molecules SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSU

#2: Protein 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal protein S2 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal protein S3 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7V3
#4: Protein 30S ribosomal protein S4 / Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S4 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S5 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S6 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P02358
#7: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S7 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P02359
#8: Protein 30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S8 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S10 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S10 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7R5
#11: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S11 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S12 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: A0A4S5B3M5
#13: Protein 30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S13 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S14 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S15 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0ADZ4
#16: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S16 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7T3
#17: Protein 30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S17 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S18 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S19 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7U3
#20: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S20 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P68679

+
50S ribosomal protein ... , 31 types, 31 molecules LBLCLDLELFLILJLKLMLNLOLPLQLRLSLTLULVLWLXLYLaLbLcLdLeLfLgLhLiLj

#25: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L2 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P60422
#26: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P60438
#27: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P60723
#28: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L5 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P62399
#29: Protein 50S ribosomal protein L6 / Large ribosomal subunit protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L6 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG55
#30: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L9 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7R1
#31: Protein 50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L10 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7J3
#32: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L11 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7J7
#33: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L13 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AA10
#34: Protein 50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L14 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0ADY3
#35: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L15 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P02413
#36: Protein 50S ribosomal protein L16


Mass: 15327.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L16 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0ADY7
#37: Protein 50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L17 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG44
#38: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L18 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0C018
#39: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L19 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7K6
#40: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L20 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7L3
#41: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L21 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG48
#42: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L22 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P61175
#43: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L23 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0ADZ0
#44: Protein 50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L24 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P60624
#45: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L25 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P68919
#46: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L27 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7L8
#47: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L28 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7M2
#48: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L29 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7M6
#49: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L30 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0AG51
#50: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L31 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7M9
#51: Protein 50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L32 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7N4
#52: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L33 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7N9
#53: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L34 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7P5
#54: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L35 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7Q1
#55: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein L36 / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: MRE600 / References: UniProt: P0A7Q6

-
Protein/peptide , 1 types, 1 molecules Pp

#57: Protein/peptide Chains: Pp


Mass: 425.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: MRE600

-
Non-polymers , 6 types, 484 molecules

#59: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#60: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 405 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#63: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#64: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RibosomeRIBOSOME#1-#580MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#21, #23-#55, #571NATURAL
3tRNA moleculesCOMPLEX#56, #581RECOMBINANT
4mRNACOMPLEX#221SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Escherichia coli K-12 (bacteria)83333MRE600
33Escherichia coli K-12 (bacteria)83333MRE600
44Escherichia coli BL21 (bacteria)511693
Source (recombinant)Organism: Escherichia coli K-12 (bacteria) / Strain: MRE600
Buffer solutionpH: 7.5
SpecimenConc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

-
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 FIELD
Image recordingElectron dose: 87 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109769 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

+
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