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- PDB-6c4i: Conformation of methylated GGQ in the peptidyl transferase center... -

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Basic information

Entry
Database: PDB / ID: 6c4i
TitleConformation of methylated GGQ in the peptidyl transferase center during translation termination
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Alternative ribosome-rescue factor A
  • E-site or P-site tRNA fMet
  • Peptide chain release factor 2
  • mRNAMessenger RNA
KeywordsRIBOSOME / nonstop / termination / ArfA / RF2 / methylation
Function / homology
Function and homology information


translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / rescue of stalled ribosome / translational termination / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translational initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / : / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain ...Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / 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 L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / 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/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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature.
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L29 / Small ribosomal subunit protein uS19 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L29 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Peptide chain release factor RF2 / 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 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 uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / 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 / Alternative ribosome-rescue factor A / 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 (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsZeng, F. / Jin, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120552 United States
CitationJournal: Sci Rep / Year: 2018
Title: Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.
Authors: Fuxing Zeng / Hong Jin /
Abstract: The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The ...The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 8, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
0: 50S ribosomal protein L30
1: 50S ribosomal protein L31
2: 50S ribosomal protein L32
3: 50S ribosomal protein L33
4: 50S ribosomal protein L34
5: 50S ribosomal protein L35
6: 50S ribosomal protein L36
a: 16S rRNA
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
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: Peptide chain release factor 2
w: Alternative ribosome-rescue factor A
x: E-site or P-site tRNA fMet
y: E-site or P-site tRNA fMet
z: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,282,070378
Polymers2,274,23459
Non-polymers7,836319
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area342420 Å2
ΔGint-5257 kcal/mol
Surface area787710 Å2

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Components

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RNA chain , 5 types, 6 molecules ABaxyz

#1: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941832.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 687670942
#2: RNA chain 5S rRNA / 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
#34: RNA chain 16S rRNA /


Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1162858853
#57: RNA chain E-site or P-site tRNA fMet


Mass: 24802.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1315725308
#58: RNA chain mRNA / Messenger RNA


Mass: 5922.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZ0123456

#3: Protein 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT2
#4: Protein 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#5: 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: P60723
#6: Protein 50S ribosomal protein L5 /


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


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#8: 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: P0A7R1
#9: Protein 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J3
#10: Protein 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#11: 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: P0AA10
#12: 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: P0ADY3
#13: 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: P02413
#14: Protein 50S ribosomal protein L16 /


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


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#16: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#17: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#18: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#19: 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: P0AG48
#20: 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: P61175
#21: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#22: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#23: 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: P68919
#24: Protein 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#25: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#26: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7M1M6
#27: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#28: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9
#29: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#30: Protein 50S ribosomal protein L33 /


Mass: 6057.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#31: 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: P0A7P5
#32: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#33: 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: P0A7Q6

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

#35: Protein 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#36: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#37: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#38: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#39: Protein 30S ribosomal protein S6 /


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#40: Protein 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#41: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#42: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#43: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#44: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#45: Protein 30S ribosomal protein S12 /


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#46: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#47: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#48: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#49: 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: P0A7T3
#50: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#51: Protein 30S ribosomal protein S18 /


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


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT1
#53: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#54: Protein 30S ribosomal protein S21 /


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

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Protein , 2 types, 2 molecules vw

#55: Protein Peptide chain release factor 2


Mass: 43384.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfB, supK, b2891, JW5847 / Production host: Escherichia coli (E. coli) / References: UniProt: P07012
#56: Protein Alternative ribosome-rescue factor A /


Mass: 6513.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arfA, yhdL, b4550, JW3253 / Production host: Escherichia coli (E. coli) / References: UniProt: P36675

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Non-polymers , 3 types, 321 molecules

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


Mass: 24.305 Da / Num. of mol.: 317 / Source method: obtained synthetically / Formula: Mg
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#61: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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
IDNameTypeEntity IDParent-IDSource
1nonstop ribosomal complex with ArfA/RF2RIBOSOME#1-#580MULTIPLE SOURCES
250S subunitProkaryotic large ribosomal subunitCOMPLEX#1-#331NATURAL
330S subunitProkaryotic small ribosomal subunitCOMPLEX#34-#541NATURAL
4Peptide chain release factor 2ORGANELLE OR CELLULAR COMPONENT#551RECOMBINANT
5Alternative ribosome-rescue factor AORGANELLE OR CELLULAR COMPONENT#561RECOMBINANT
6E-site or P-site tRNA fMetORGANELLE OR CELLULAR COMPONENT#571RECOMBINANT
7nonstop mRNAORGANELLE OR CELLULAR COMPONENT#581RECOMBINANT
823S rRNA23S ribosomal RNAORGANELLE OR CELLULAR COMPONENT#12NATURAL
95S rRNA5S ribosomal RNAORGANELLE OR CELLULAR COMPONENT#22NATURAL
1016S rRNAORGANELLE OR CELLULAR COMPONENT#343NATURAL
1130S ribosomal proteinsRibosomal proteinCOMPLEX#35-#543NATURAL
1250S ribosomal proteinsRibosomal proteinCOMPLEX#3-#332NATURAL
1350S ribosomal protein L2ORGANELLE OR CELLULAR COMPONENT#312NATURAL
1450S ribosomal protein L3ORGANELLE OR CELLULAR COMPONENT#412NATURAL
1550S ribosomal protein L4ORGANELLE OR CELLULAR COMPONENT#512NATURAL
1650S ribosomal protein L5ORGANELLE OR CELLULAR COMPONENT#612NATURAL
1750S ribosomal protein L6ORGANELLE OR CELLULAR COMPONENT#712NATURAL
1850S ribosomal protein L9ORGANELLE OR CELLULAR COMPONENT#812NATURAL
1950S ribosomal protein L10ORGANELLE OR CELLULAR COMPONENT#912NATURAL
2050S ribosomal protein L11ORGANELLE OR CELLULAR COMPONENT#1012NATURAL
2150S ribosomal protein L13ORGANELLE OR CELLULAR COMPONENT#1112NATURAL
2250S ribosomal protein L14ORGANELLE OR CELLULAR COMPONENT#1212NATURAL
2350S ribosomal protein L15ORGANELLE OR CELLULAR COMPONENT#1312NATURAL
2450S ribosomal protein L16ORGANELLE OR CELLULAR COMPONENT#1412NATURAL
2550S ribosomal protein L17ORGANELLE OR CELLULAR COMPONENT#1512NATURAL
2650S ribosomal protein L18ORGANELLE OR CELLULAR COMPONENT#1612NATURAL
2750S ribosomal protein L19ORGANELLE OR CELLULAR COMPONENT#1712NATURAL
2850S ribosomal protein L20ORGANELLE OR CELLULAR COMPONENT#1812NATURAL
2950S ribosomal protein L21ORGANELLE OR CELLULAR COMPONENT#1912NATURAL
3050S ribosomal protein L22ORGANELLE OR CELLULAR COMPONENT#2012NATURAL
3150S ribosomal protein L23ORGANELLE OR CELLULAR COMPONENT#2112NATURAL
3250S ribosomal protein L24ORGANELLE OR CELLULAR COMPONENT#2212NATURAL
3350S ribosomal protein L25ORGANELLE OR CELLULAR COMPONENT#2312NATURAL
3450S ribosomal protein L27ORGANELLE OR CELLULAR COMPONENT#2412NATURAL
3550S ribosomal protein L28ORGANELLE OR CELLULAR COMPONENT#2512NATURAL
3650S ribosomal protein L29ORGANELLE OR CELLULAR COMPONENT#2612NATURAL
3750S ribosomal protein L30ORGANELLE OR CELLULAR COMPONENT#2712NATURAL
3850S ribosomal protein L31ORGANELLE OR CELLULAR COMPONENT#2812NATURAL
3950S ribosomal protein L32ORGANELLE OR CELLULAR COMPONENT#2912NATURAL
4050S ribosomal protein L33ORGANELLE OR CELLULAR COMPONENT#3012NATURAL
4150S ribosomal protein L34ORGANELLE OR CELLULAR COMPONENT#3112NATURAL
4250S ribosomal protein L35ORGANELLE OR CELLULAR COMPONENT#3212NATURAL
4350S ribosomal protein L36ORGANELLE OR CELLULAR COMPONENT#3312NATURAL
4430S ribosomal protein S2ORGANELLE OR CELLULAR COMPONENT#3511NATURAL
4530S ribosomal protein S3ORGANELLE OR CELLULAR COMPONENT#3611NATURAL
4630S ribosomal protein S4ORGANELLE OR CELLULAR COMPONENT#3711NATURAL
4730S ribosomal protein S5ORGANELLE OR CELLULAR COMPONENT#3811NATURAL
4830S ribosomal protein S6ORGANELLE OR CELLULAR COMPONENT#3911NATURAL
4930S ribosomal protein S7ORGANELLE OR CELLULAR COMPONENT#4011NATURAL
5030S ribosomal protein S8ORGANELLE OR CELLULAR COMPONENT#4111NATURAL
5130S ribosomal protein S9ORGANELLE OR CELLULAR COMPONENT#4211NATURAL
5230S ribosomal protein S10ORGANELLE OR CELLULAR COMPONENT#4311NATURAL
5330S ribosomal protein S11ORGANELLE OR CELLULAR COMPONENT#4411NATURAL
5430S ribosomal protein S12ORGANELLE OR CELLULAR COMPONENT#4511NATURAL
5530S ribosomal protein S13ORGANELLE OR CELLULAR COMPONENT#4611NATURAL
5630S ribosomal protein S14ORGANELLE OR CELLULAR COMPONENT#4711NATURAL
5730S ribosomal protein S15ORGANELLE OR CELLULAR COMPONENT#4811NATURAL
5830S ribosomal protein S16ORGANELLE OR CELLULAR COMPONENT#4911NATURAL
5930S ribosomal protein S17ORGANELLE OR CELLULAR COMPONENT#5011NATURAL
6030S ribosomal protein S18ORGANELLE OR CELLULAR COMPONENT#5111NATURAL
6130S ribosomal protein S19ORGANELLE OR CELLULAR COMPONENT#5211NATURAL
6230S ribosomal protein S20ORGANELLE OR CELLULAR COMPONENT#5311NATURAL
6330S ribosomal protein S21ORGANELLE OR CELLULAR COMPONENT#5411NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
44Escherichia coli (E. coli)562
55Escherichia coli (E. coli)562
66Escherichia coli (E. coli)562
77Escherichia coli (E. coli)562
88Escherichia coli (E. coli)562
99Escherichia coli (E. coli)562
1010Escherichia coli (E. coli)562
1111Escherichia coli (E. coli)562
1212Escherichia coli (E. coli)562
1313Escherichia coli (E. coli)562
1414Escherichia coli (E. coli)562
1515Escherichia coli (E. coli)562
1616Escherichia coli (E. coli)562
1717Escherichia coli (E. coli)562
1818Escherichia coli (E. coli)562
1919Escherichia coli (E. coli)562
2020Escherichia coli (E. coli)562
2121Escherichia coli (E. coli)562
2222Escherichia coli (E. coli)562
2323Escherichia coli (E. coli)562
2424Escherichia coli (E. coli)562
2525Escherichia coli (E. coli)562
2626Escherichia coli (E. coli)562
2727Escherichia coli (E. coli)562
2828Escherichia coli (E. coli)562
2929Escherichia coli (E. coli)562
3030Escherichia coli (E. coli)562
3131Escherichia coli (E. coli)562
3232Escherichia coli (E. coli)562
3333Escherichia coli (E. coli)562
3434Escherichia coli (E. coli)562
3535Escherichia coli (E. coli)562
3636Escherichia coli (E. coli)562
3737Escherichia coli (E. coli)562
3838Escherichia coli (E. coli)562
3939Escherichia coli (E. coli)562
4040Escherichia coli (E. coli)562
4141Escherichia coli (E. coli)562
4242Escherichia coli (E. coli)562
4343Escherichia coli (E. coli)562
4444Escherichia coli (E. coli)562
4545Escherichia coli (E. coli)562
4646Escherichia coli (E. coli)562
4747Escherichia coli (E. coli)562
4848Escherichia coli (E. coli)562
4949Escherichia coli (E. coli)562
5050Escherichia coli (E. coli)562
5151Escherichia coli (E. coli)562
5252Escherichia coli (E. coli)562
5353Escherichia coli (E. coli)562
5454Escherichia coli (E. coli)562
5555Escherichia coli (E. coli)562
5656Escherichia coli (E. coli)562
5757Escherichia coli (E. coli)562
5858Escherichia coli (E. coli)562
5959Escherichia coli (E. coli)562
6060Escherichia coli (E. coli)562
6161Escherichia coli (E. coli)562
6262Escherichia coli (E. coli)562
6363Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
24Escherichia coli (E. coli)562
35Escherichia coli (E. coli)562
46Escherichia coli (E. coli)562
57Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidC8H18N2O4S1
215 mMmagnesium acetateMg(CH3COO)21
3150 mMpotassium acetateCH3CO2K1
44 mMbeta-mercapthoethanolHOCH2CH2SH1
52 mMspermidineC7H19N31
60.05 mMsperminC10H26N41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/0.5 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Grids were blotted for 3.5 seconds.

-
Electron microscopy imaging

MicroscopyModel: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 83822 X
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 20 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND4CTF correction
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143372 / Symmetry type: POINT

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