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- PDB-5u9g: 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I) -

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Entry
Database: PDB / ID: 5u9g
Title3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Alternative ribosome-rescue factor A
  • Peptide chain release factor RF2
  • fMet-tRNA (P- and E-site)
  • truncated mRNA
KeywordsRIBOSOME / ARFA RF2 ribosome rescue complex
Function / homologyRibosomal protein L22/L17 superfamily / Ribosomal protein L25 / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 ...Ribosomal protein L22/L17 superfamily / Ribosomal protein L25 / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L28/L24 / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / RNA-binding S4 domain 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 L14 superfamily / Ribosomal protein L17 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein L33 superfamily / 30S ribosomal protein S17 / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L9, N-terminal / Ribosomal protein L9, C-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25, short-form / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S11, bacterial-type / Ribosomal protein S7, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L11, C-terminal / Ribosomal protein L4 domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L13, conserved site / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L10 / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal protein L35 / Ribosomal protein L11, N-terminal / Ribosomal protein L18e/L15P / Ribosomal protein L34, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L16, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein S21 superfamily / Ribosomal protein L19 superfamily / Ribosomal protein S14, conserved site / PCRF domain / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / KH domain / Ribosomal protein L9, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L11, N-terminal domain / Domain of unknown function / Ribosomal protein S5, C-terminal domain / Ribosomal L32p protein family
Function and homology information
Specimen sourceEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsDemo, G. / Svidritskiy, E. / Madireddy, R. / Diaz-Avalos, R. / Grant, T. / Grigorieff, N. / Sousa, D. / Korostelev, A.A.
CitationJournal: Elife / Year: 2017
Title: Mechanism of ribosome rescue by ArfA and RF2.
Authors: Gabriel Demo / Egor Svidritskiy / Rohini Madireddy / Ruben Diaz-Avalos / Timothy Grant / Nikolaus Grigorieff / Duncan Sousa / Andrei A Korostelev
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 16, 2016 / Release: Mar 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelDatabase references
1.2Sep 27, 2017Structure modelAuthor supporting evidence / Data collection / Experimental preparationem_sample_support / em_software / pdbx_audit_support_em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 16S ribosomal RNA
01: 23S ribosomal RNA
02: 5S ribosomal RNA
Y: Alternative ribosome-rescue factor A
X: fMet-tRNA (P- and E-site)
03: 50S ribosomal protein L1
04: 50S ribosomal protein L2
05: 50S ribosomal protein L3
06: 50S ribosomal protein L4
07: 50S ribosomal protein L5
08: 50S ribosomal protein L6
09: 50S ribosomal protein L9
10: 50S ribosomal protein L10
11: 50S ribosomal protein L11
12: 50S ribosomal protein L13
13: 50S ribosomal protein L14
14: 50S ribosomal protein L15
15: 50S ribosomal protein L16
16: 50S ribosomal protein L17
17: 50S ribosomal protein L18
18: 50S ribosomal protein L19
19: 50S ribosomal protein L20
20: 50S ribosomal protein L21
21: 50S ribosomal protein L22
22: 50S ribosomal protein L23
23: 50S ribosomal protein L24
24: 50S ribosomal protein L25
25: 50S ribosomal protein L27
26: 50S ribosomal protein L28
27: 50S ribosomal protein L29
28: 50S ribosomal protein L30
29: 50S ribosomal protein L31
30: 50S ribosomal protein L32
31: 50S ribosomal protein L33
32: 50S ribosomal protein L34
33: 50S ribosomal protein L35
34: 50S ribosomal protein L36
V: truncated mRNA
W: fMet-tRNA (P- and E-site)
Z: Peptide chain release factor RF2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,305,207409
Polyers2,296,68460
Non-polymers8,524349
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 , 5 types, 6 molecules A0102XWV

#1: RNA chain 16S ribosomal RNA /


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 944404559
#2: RNA chain 23S ribosomal RNA /


Mass: 941322.188 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 42756
#3: RNA chain 5S ribosomal RNA /


Mass: 38483.926 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1072784372
#5: RNA chain fMet-tRNA (P- and E-site)


Mass: 24802.785 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 1114191980
#38: RNA chain truncated mRNA


Mass: 4597.844 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli (E. coli)

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Protein/peptide , 2 types, 2 molecules YZ

#4: Protein/peptide Alternative ribosome-rescue factor A /


Mass: 8190.438 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: arfA, yhdL, b4550, JW3253 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P36675
#39: Protein/peptide Peptide chain release factor RF2 / RF-2


Mass: 41300.660 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: prfB, supK, b2891, JW5847 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P07012

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50S ribosomal protein ... , 32 types, 32 molecules 0304050607080910111213141516171819202122232425262728293031323334

#6: Protein/peptide 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIX0, UniProt: P0A7L0*PLUS
#7: Protein/peptide 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F8, UniProt: P60422*PLUS
#8: Protein/peptide 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F5, UniProt: P60438*PLUS
#9: Protein/peptide 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F6, UniProt: P60723*PLUS
#10: Protein/peptide 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G7, UniProt: P62399*PLUS
#11: Protein/peptide 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H0, UniProt: P0AG55*PLUS
#12: Protein/peptide 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZI15, UniProt: P0A7R1*PLUS
#13: Protein/peptide 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZA73, UniProt: P0A7J3*PLUS
#14: Protein/peptide 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZA71, UniProt: P0A7J7*PLUS
#15: Protein/peptide 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZET0, UniProt: P0AA10*PLUS
#16: Protein/peptide 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G5, UniProt: P0ADY3*PLUS
#17: Protein/peptide 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D8BU19, UniProt: P02413*PLUS
#18: Protein/peptide 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G2, UniProt: P0ADY7*PLUS
#19: Protein/peptide 50S ribosomal protein L17 /


Mass: 14423.683 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7N179, UniProt: P0AG44*PLUS
#20: Protein/peptide 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H1, UniProt: P0C018*PLUS
#21: Protein/peptide 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZKU3, UniProt: P0A7K6*PLUS
#22: Protein/peptide 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MAS6, UniProt: P0A7L3*PLUS
#23: Protein/peptide 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZEN7, UniProt: P0AG48*PLUS
#24: Protein/peptide 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G0, UniProt: P61175*PLUS
#25: Protein/peptide 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7X2Z9, UniProt: P0ADZ0*PLUS
#26: Protein/peptide 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G6, UniProt: P60624*PLUS
#27: Protein/peptide 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7XH79, UniProt: P68919*PLUS
#28: Protein/peptide 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZEN6, UniProt: P0A7L8*PLUS
#29: Protein/peptide 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: S0YB49, UniProt: P0A7M2*PLUS
#30: Protein/peptide 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G3, UniProt: P0A7M6*PLUS
#31: Protein/peptide 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H3, UniProt: P0AG51*PLUS
#32: Protein/peptide 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZFP6, UniProt: P0A7M9*PLUS
#33: Protein/peptide 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZGG2, UniProt: P0A7N4*PLUS
#34: Protein/peptide 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9P0, UniProt: P0A7N9*PLUS
#35: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MGC4, UniProt: P0A7P5*PLUS
#36: Protein/peptide 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z814, UniProt: P0A7Q1*PLUS
#37: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L017, UniProt: P0A7Q6*PLUS

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

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


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZK99, UniProt: P0A7V0*PLUS
#41: Protein/peptide 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS9, UniProt: P0A7V3*PLUS
#42: Protein/peptide 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H7, UniProt: P0A7V8*PLUS
#43: Protein/peptide 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H2, UniProt: P0A7W1*PLUS
#44: Protein/peptide 30S ribosomal protein S6 /


Mass: 15211.058 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZI17, UniProt: P02358*PLUS
#45: Protein/peptide 30S ribosomal protein S7 /


Mass: 17637.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAN1, UniProt: P02359*PLUS
#46: Protein/peptide 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G9, UniProt: P0A7W7*PLUS
#47: Protein/peptide 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZES9, UniProt: P0A7X3*PLUS
#48: Protein/peptide 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F4, UniProt: P0A7R5*PLUS
#49: Protein/peptide 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCR3, UniProt: P0A7R9*PLUS
#50: Protein/peptide 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAN0, UniProt: P0A7S3*PLUS
#51: Protein/peptide 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: H4UQ02, UniProt: P0A7S9*PLUS
#52: Protein/peptide 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G8, UniProt: P0AG59*PLUS
#53: Protein/peptide 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZEL4, UniProt: P0ADZ4*PLUS
#54: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MIU7, UniProt: P0A7T3*PLUS
#55: Protein/peptide 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G4, UniProt: P0AG63*PLUS
#56: Protein/peptide 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2KXL3, UniProt: P0A7T7*PLUS
#57: Protein/peptide 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F9, UniProt: P0A7U3*PLUS
#58: Protein/peptide 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAS2, UniProt: P0A7U7*PLUS
#59: Protein/peptide 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L2J1, UniProt: P68679*PLUS

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Non-polymers , 2 types, 349 molecules

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


Mass: 24.305 Da / Num. of mol.: 348 / Formula: Mg / Magnesium
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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

ComponentName: ArfA-RF2 ribosome rescue complex (Structure I) / Type: RIBOSOME
Entity ID: 1, 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
Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: K-12
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTris bufferTris-HCl1
2100 mMamonium chlorideNH4Cl1
320 mMmagnesium chlorideMgCl21
40.5 mMEthylenediaminetetraacetic acidEDTA1
56 mMbetamercaptoethanolBME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Using a Solarus 950 plasma cleaning system. The forward RF target was set to 7w.
Grid material: COPPER / Grid mesh size: 200 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number of grids imaged: 1 / Number of real images: 3760
Image scansMovie frames/image: 54 / Used frames/image: 2-27

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2Leginonimage acquisition
4ctffind4CTF correction
7Chimeramodel fitting
9RSRefmodel refinement
10PHENIXmodel refinement
11FREALIGN9.11initial Euler assignment
12FREALIGN9.11final Euler assignment
13FREALIGN9.11classification
14FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 539311
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 139861 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 100 / Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation coefficient

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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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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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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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