[English] 日本語
Yorodumi
- PDB-6ore: Release complex 70S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ore
TitleRelease complex 70S
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • FME-PHE-PHE
  • P-tRNA
  • RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')
KeywordsRIBOSOME / Time-resolved cryo-EM / Termination / short-lived / millisecond
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity ...mRNA binding involved in posttranscriptional gene silencing / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / four-way junction DNA binding / negative regulation of translational initiation / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / translational initiation / polysomal ribosome / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / ribosome assembly / endodeoxyribonuclease activity / DNA-templated transcription, termination / positive regulation of translational fidelity / maintenance of translational fidelity / response to reactive oxygen species / regulation of cell growth / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / regulation of mRNA stability / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / regulation of translation / ribosome binding / ribosomal large subunit assembly / ribosome biogenesis / response to radiation / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 superfamily ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 superfamily / Ribosomal protein S16 signature. / Ribosomal protein S16, conserved site / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L28/L24 superfamily / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L19 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L20 signature. / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6 signature. / Ribosomal protein S6, conserved site / Ribosomal protein L14P, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L34 / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S4, bacterial-type / Ribosomal L28 family / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / L28p-like / Ribosomal L32p protein family / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L16
Similarity search - Domain/homology
50S ribosomal protein L33 / 30S ribosomal protein S18 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S3 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S19 ...50S ribosomal protein L33 / 30S ribosomal protein S18 / 30S ribosomal protein S9 / 30S ribosomal protein S8 / 30S ribosomal protein S5 / 30S ribosomal protein S4 / 30S ribosomal protein S3 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S19 / 50S ribosomal protein L31 / 30S ribosomal protein S16 / 50S ribosomal protein L14 / 30S ribosomal protein S13 / 30S ribosomal protein S12 / 30S ribosomal protein S11 / 30S ribosomal protein S10 / 50S ribosomal protein L9 / 50S ribosomal protein L36 / 50S ribosomal protein L32 / 50S ribosomal protein L35 / 50S ribosomal protein L34 / 50S ribosomal protein L13 / 50S ribosomal protein L3 / 50S ribosomal protein L16 / 50S ribosomal protein L22 / 30S ribosomal protein S13 / 30S ribosomal protein S9 / 50S ribosomal protein L27 / 50S ribosomal protein L5 / 50S ribosomal protein L28 / 50S ribosomal protein L20 / 30S ribosomal protein S7 / 50S ribosomal protein L25 / 30S ribosomal protein S21 / 50S ribosomal protein L5 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L24 / 50S ribosomal protein L2 / 50S ribosomal protein L18 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 50S ribosomal protein L6 / 50S ribosomal protein L30 / 50S ribosomal protein L21 / 50S ribosomal protein L17 / 30S ribosomal protein S15 / 50S ribosomal protein L29 / : / 50S ribosomal protein L27 / 50S ribosomal protein L36 / : / 30S ribosomal protein S6 / 30S ribosomal protein S3 / 50S ribosomal protein L17 / 50S ribosomal protein L29 / 50S ribosomal protein L6 / 50S ribosomal protein L24 / 50S ribosomal protein L32 / 50S ribosomal protein L18 / : / 30S ribosomal protein S2 / 30S ribosomal protein S17 / 50S ribosomal protein L31 / 30S ribosomal protein S5 / 50S ribosomal protein L15 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / RNA (> 1000) / RNA (> 100) / RNA (> 10) / RNA / 30S ribosomal protein S16 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 30S ribosomal protein S20 / 50S ribosomal protein L19 / 50S ribosomal protein L15 / 30S ribosomal protein S7 / 30S ribosomal protein S6 / 30S ribosomal protein S12 / 30S ribosomal protein S4 / 30S ribosomal protein S21 / 30S ribosomal protein S10 / 30S ribosomal protein S14 / 50S ribosomal protein L30 / 50S ribosomal protein L35 / 50S ribosomal protein L25 / 50S ribosomal protein L33 / 30S ribosomal protein S8 / 30S ribosomal protein S18 / 50S ribosomal protein L9 / 50S ribosomal protein L13 / 50S ribosomal protein L21 / 50S ribosomal protein L14 / 50S ribosomal protein L22 / 50S ribosomal protein L4 / 30S ribosomal protein S15 / 50S ribosomal protein L28
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFu, Z.
Funding support United States, Sweden, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 United States
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2019
Title: The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.
Authors: Ziao Fu / Gabriele Indrisiunaite / Sandip Kaledhonkar / Binita Shah / Ming Sun / Bo Chen / Robert A Grassucci / Måns Ehrenberg / Joachim Frank /
Abstract: When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in ...When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20173
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 23S ribosomal RNA
2: 16S ribosomal RNA
3: 5S ribosomal RNA
4: RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')
5: P-tRNA
A: FME-PHE-PHE
B: 50S ribosomal protein L2
C: 50S ribosomal protein L3
D: 50S ribosomal protein L4
E: 50S ribosomal protein L5
F: 50S ribosomal protein L6
G: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 50S ribosomal protein L31
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 30S ribosomal protein S2
h: 30S ribosomal protein S3
i: 30S ribosomal protein S4
j: 30S ribosomal protein S5
k: 30S ribosomal protein S6
l: 30S ribosomal protein S7
m: 30S ribosomal protein S8
n: 30S ribosomal protein S9
o: 30S ribosomal protein S10
p: 30S ribosomal protein S11
q: 30S ribosomal protein S12
r: 30S ribosomal protein S13
s: 30S ribosomal protein S14
t: 30S ribosomal protein S15
u: 30S ribosomal protein S16
v: 30S ribosomal protein S17
w: 30S ribosomal protein S18
x: 30S ribosomal protein S19
y: 30S ribosomal protein S20
z: 30S ribosomal protein S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,152,755493
Polymers2,142,02755
Non-polymers10,728438
Water0
1


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

-
Components

-
RNA chain , 5 types, 5 molecules 12345

#1: RNA chain 23S ribosomal RNA /


Mass: 941526.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain 16S ribosomal RNA /


Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1273279017
#4: RNA chain RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')


Mass: 2754.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain P-tRNA


Mass: 24565.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

-
Protein/peptide , 1 types, 1 molecules A

#6: Protein/peptide FME-PHE-PHE


Mass: 471.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

+
50S ribosomal protein ... , 29 types, 29 molecules BCDEFGJKLMNOPQRSTUVWXYZabcdef

#7: Protein 50S ribosomal protein L2 /


Mass: 29663.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A029IK04, UniProt: P60422*PLUS
#8: 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 (E. coli) / References: UniProt: P60438
#9: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F6, UniProt: P60723*PLUS
#10: Protein 50S ribosomal protein L5 /


Mass: 20073.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: V0AXZ0, UniProt: P62399*PLUS
#11: Protein 50S ribosomal protein L6 /


Mass: 18672.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A1X3JB47, UniProt: P0AG55*PLUS
#12: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZI15, UniProt: P0A7R1*PLUS
#13: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZET0, UniProt: P0AA10*PLUS
#14: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G5, UniProt: P0ADY3*PLUS
#15: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6, UniProt: P02413*PLUS
#16: Protein 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#17: Protein 50S ribosomal protein L17 /


Mass: 13592.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2T1LEK9, UniProt: P0AG44*PLUS
#18: Protein 50S ribosomal protein L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0F6C9R0, UniProt: P0C018*PLUS
#19: Protein 50S ribosomal protein L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: D6IC61, UniProt: P0A7K6*PLUS
#20: Protein 50S ribosomal protein L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: S1EK76, UniProt: P0A7L3*PLUS
#21: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZEN7, UniProt: P0AG48*PLUS
#22: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G0, UniProt: P61175*PLUS
#23: Protein 50S ribosomal protein L23 /


Mass: 10661.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A029IKB7, UniProt: P0ADZ0*PLUS
#24: Protein 50S ribosomal protein L24 /


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0G3K7Z5, UniProt: P60624*PLUS
#25: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XH79, UniProt: P68919*PLUS
#26: Protein 50S ribosomal protein L27 /


Mass: 8275.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: U9XYH0, UniProt: P0A7L8*PLUS
#27: Protein 50S ribosomal protein L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: V8F9Y0, UniProt: P0A7M2*PLUS
#28: Protein 50S ribosomal protein L29 /


Mass: 7155.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3JBH6, UniProt: P0A7M6*PLUS
#29: Protein 50S ribosomal protein L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7R6H0, UniProt: P0AG51*PLUS
#30: Protein 50S ribosomal protein L31 /


Mass: 7516.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A080FR68, UniProt: P0A7M9*PLUS
#31: Protein 50S ribosomal protein L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0G3K5Y7, UniProt: P0A7N4*PLUS
#32: Protein 50S ribosomal protein L33 /


Mass: 6057.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: H4LIZ0, UniProt: P0A7N9*PLUS
#33: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MGC4, UniProt: P0A7P5*PLUS
#34: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: I2RJ64, UniProt: P0A7Q1*PLUS
#35: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L017, UniProt: P0A7Q6*PLUS

+
30S ribosomal protein ... , 20 types, 20 molecules ghijklmnopqrstuvwxyz

#36: Protein 30S ribosomal protein S2 /


Mass: 25072.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2, UniProt: P0A7V0*PLUS
#37: Protein 30S ribosomal protein S3 /


Mass: 23248.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376HTV6, UniProt: P0A7V3*PLUS
#38: Protein 30S ribosomal protein S4 /


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L3PZ69, UniProt: P0A7V8*PLUS
#39: Protein 30S ribosomal protein S5 /


Mass: 16475.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A073FR78, UniProt: P0A7W1*PLUS
#40: Protein 30S ribosomal protein S6 /


Mass: 12125.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376ZL25, UniProt: P02358*PLUS
#41: Protein 30S ribosomal protein S7 /


Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1D5F0, UniProt: P02359*PLUS
#42: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D8A1L7, UniProt: P0A7W7*PLUS
#43: Protein 30S ribosomal protein S9 /


Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T9TH92, UniProt: P0A7X3*PLUS
#44: Protein 30S ribosomal protein S10 /


Mass: 11254.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7RLQ6, UniProt: P0A7R5*PLUS
#45: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#46: Protein 30S ribosomal protein S12 /


Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: L4V1L2, UniProt: P0A7S3*PLUS
#47: Protein 30S ribosomal protein S13 /


Mass: 12868.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T6LFY5, UniProt: P0A7S9*PLUS
#48: Protein 30S ribosomal protein S14 /


Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7R6H7, UniProt: P0AG59*PLUS
#49: Protein 30S ribosomal protein S15 /


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XN21, UniProt: P0ADZ4*PLUS
#50: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7, UniProt: P0A7T3*PLUS
#51: Protein 30S ribosomal protein S17 /


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080IK26, UniProt: P0AG63*PLUS
#52: Protein 30S ribosomal protein S18 /


Mass: 7734.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: D7ZI16, UniProt: P0A7T7*PLUS
#53: Protein 30S ribosomal protein S19 /


Mass: 9421.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0A8UF41, UniProt: P0A7U3*PLUS
#54: Protein 30S ribosomal protein S20 /


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: I4T5W9, UniProt: P0A7U7*PLUS
#55: Protein 30S ribosomal protein S21 /


Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: L3C5D9, UniProt: P68679*PLUS

-
Non-polymers , 2 types, 438 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 436 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Release complex 70S ribosomes / Type: RIBOSOME / Entity ID: #1-#4, #7-#55 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 41.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135250 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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