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- PDB-6q95: Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ri... -

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Entry
Database: PDB / ID: 6q95
TitleStructure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • Nascent peptide MET-ALA
  • SsrA-binding protein
  • mRNAMessenger RNA
  • tRNA-Phe
  • tRNA-fMet
  • transfer-messenger RNA (tmRNA)
KeywordsRIBOSOME / tmRNA SmpB trans-translation translation
Function / homologyRibosomal protein L20, C-terminal / Ribosomal protein L14 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L25, C-terminal ...Ribosomal protein L20, C-terminal / Ribosomal protein L14 superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein S7 domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein S19 / Ribosomal protein L33 superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein L19 superfamily / Ribosomal protein L17 superfamily / L21-like superfamily / Ribosomal protein S2 / Ribosomal protein L13, conserved site / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Small protein B / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein S14, type Z / Ribosomal protein S16 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7 domain / Ribosomal protein L28/L24 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L5, N-terminal / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20 signature. / L28p-like / 30S ribosomal protein Thx / Ribosomal protein L5, C-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein L15 / 30S ribosomal protein / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / Ribosomal protein S15 / Ribosomal protein L30p/L7e / Ribosomal protein L18e/L15P / Ribosomal protein S8 signature. / Ribosomal protein L5 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 30S ribosomal protein Thx / Ribosomal protein TL5, C-terminal domain / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature. / Ribosomal protein L13 signature. / Ribosomal protein L9 signature. / Ribosomal protein S13 signature. / Ribosomal protein L30 signature. / Ribosomal protein S5 signature.
Function and homology information
Specimen sourceThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsRae, C.D.
CitationJournal: Science / Year: 2019
Title: How a circularized tmRNA moves through the ribosome.
Authors: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan
Abstract: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 17, 2018 / Release: Feb 27, 2019

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Structure visualization

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Assembly

Deposited unit
2: 16S RIBOSOMAL RNA
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 type Z
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 Thx
7: tRNA-fMet
8: tRNA-Phe
9: mRNA
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
1: 23S RIBOSOMAL RNA
3: 5S RIBOSOMAL RNA
A: 50S ribosomal protein L1
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
5: SsrA-binding protein
6: Nascent peptide MET-ALA
f: 50S ribosomal protein L36
H: 50S RIBOSOMAL PROTEIN L10 AND L11
I: 50S RIBOSOMAL PROTEIN L10 AND L11
4: transfer-messenger RNA (tmRNA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,359,512701
Polyers2,343,83361
Non-polymers15,679640
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 7 types, 7 molecules 2789134

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 493958.281 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#22: RNA chain tRNA-fMet


Mass: 24816.811 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#23: RNA chain tRNA-Phe


Mass: 24400.418 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli)
#24: RNA chain mRNA / Messenger RNA


Mass: 1853.133 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli (E. coli)
#34: RNA chain 23S RIBOSOMAL RNA /


Mass: 947935.438 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
#35: RNA chain 5S RIBOSOMAL RNA /


Mass: 38553.000 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: GenBank: 55771382
#60: RNA chain transfer-messenger RNA (tmRNA)


Mass: 112818.945 Da / Num. of mol.: 1
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Production host: Escherichia coli (E. coli)

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

#2: Protein/peptide 30S ribosomal protein S2 /


Mass: 27116.385 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80371
#3: Protein/peptide 30S ribosomal protein S3 /


Mass: 22975.588 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80372
#4: Protein/peptide 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80373
#5: Protein/peptide 30S ribosomal protein S5 /


Mass: 16460.193 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ5
#6: Protein/peptide 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP8
#7: Protein/peptide 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P17291
#8: Protein/peptide 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY9
#9: Protein/peptide 30S ribosomal protein S9 /


Mass: 14298.466 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80374
#10: Protein/peptide 30S ribosomal protein S10 /


Mass: 11398.308 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN7
#11: Protein/peptide 30S ribosomal protein S11 /


Mass: 12606.369 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80376
#12: Protein/peptide 30S ribosomal protein S12 /


Mass: 13875.388 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN3
#13: Protein/peptide 30S ribosomal protein S13 /


Mass: 13623.920 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80377
#14: Protein/peptide 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY6
#15: Protein/peptide 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJ76
#16: Protein/peptide 30S ribosomal protein S16 /


Mass: 9995.546 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJH3
#17: Protein/peptide 30S ribosomal protein S17 /


Mass: 11880.098 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY7
#18: Protein/peptide 30S ribosomal protein S18 /


Mass: 8155.812 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ0
#19: Protein/peptide 30S ribosomal protein S19 /


Mass: 9006.486 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP2
#20: Protein/peptide 30S ribosomal protein S20 /


Mass: 10921.086 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3089.655 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SIH3

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50S ribosomal protein ... , 31 types, 32 molecules WXYZabcdeABCDEFGJKLMNOPQRSTUVfHI

#25: Protein/peptide 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60493
#26: Protein/peptide 50S ribosomal protein L28 /


Mass: 9985.846 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60494
#27: Protein/peptide 50S ribosomal protein L29 /


Mass: 6112.247 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP6
#28: Protein/peptide 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ6
#29: Protein/peptide 50S ribosomal protein L31 /


Mass: 6640.646 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SJE1
#30: Protein/peptide 50S ribosomal protein L32 /


Mass: 6590.854 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80339
#31: Protein/peptide 50S ribosomal protein L33 /


Mass: 5602.612 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P35871
#32: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P80340
#33: Protein/peptide 50S ribosomal protein L35 /


Mass: 7374.981 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SKU1
#36: Protein/peptide 50S ribosomal protein L1 /


Mass: 24872.721 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLP7
#37: Protein/peptide 50S ribosomal protein L2 /


Mass: 29985.799 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60405
#38: Protein/peptide 50S ribosomal protein L3 /


Mass: 22321.031 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN8
#39: Protein/peptide 50S ribosomal protein L4 / / L1e


Mass: 23071.721 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHN9
#40: Protein/peptide 50S ribosomal protein L5 /


Mass: 20930.400 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ0
#41: Protein/peptide 50S ribosomal protein L6 /


Mass: 17476.279 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P0DOY8
#42: Protein/peptide 50S ribosomal protein L9 /


Mass: 6536.709 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SLQ1
#43: Protein/peptide 50S ribosomal protein L13 /


Mass: 15828.771 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60488
#44: Protein/peptide 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP8
#45: Protein/peptide 50S ribosomal protein L15 /


Mass: 15858.526 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ7
#46: Protein/peptide 50S ribosomal protein L16 /


Mass: 15364.050 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60489
#47: Protein/peptide 50S ribosomal protein L17 /


Mass: 13618.952 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q9Z9H5
#48: Protein/peptide 50S ribosomal protein L18 / / TL24


Mass: 10998.918 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHQ4
#49: Protein/peptide 50S ribosomal protein L19 /


Mass: 16289.891 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60490
#50: Protein/peptide 50S ribosomal protein L20 /


Mass: 13648.081 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60491
#51: Protein/peptide 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: P60492
#52: Protein/peptide 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP3
#53: Protein/peptide 50S ribosomal protein L23 /


Mass: 10386.274 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP0
#54: Protein/peptide 50S ribosomal protein L24 /


Mass: 11181.658 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHP9
#55: Protein/peptide 50S ribosomal protein L25 / / TL5


Mass: 10954.641 Da / Num. of mol.: 1
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SHZ1
#58: Protein/peptide 50S ribosomal protein L36 /


Mass: 4435.411 Da / Num. of mol.: 1
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Gene: rpmJ, TT_C1304 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72I28
#59: Protein/peptide 50S RIBOSOMAL PROTEIN L10 AND L11 / Ribosome


Mass: 11932.701 Da / Num. of mol.: 2
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Protein/peptide , 2 types, 2 molecules 56

#56: Protein/peptide SsrA-binding protein / Small protein B


Mass: 16785.490 Da / Num. of mol.: 1
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: smpB, TTHA0902 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RR57
#57: Protein/peptide Nascent peptide MET-ALA


Mass: 220.289 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 640 molecules

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


Mass: 24.305 Da / Num. of mol.: 637 / Formula: Mg / Magnesium
#62: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
170S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 600MULTIPLE SOURCES
270S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME56, 601RECOMBINANT
370S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME571RECOMBINANT
470S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME581RECOMBINANT
570S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 591NATURAL
670S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME22, 231NATURAL
770S ribosome bound by tmRNA-SmpB in the A siteRIBOSOME241RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12300852Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
23562Escherichia coli (E. coli)
34262724Thermus thermophilus HB27 (bacteria)
45300852Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
56562Escherichia coli (E. coli)
67562Escherichia coli (E. coli)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
33562Escherichia coli (E. coli)
44562Escherichia coli (E. coli)
6732630synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: 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: 42 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24400 / Symmetry type: POINT

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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. See below links for details.
  • 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

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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

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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.

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

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