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- PDB-3jcd: Structure of Escherichia coli EF4 in posttranslocational ribosome... -

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Basic information

Entry
Database: PDB / ID: 3jcd
TitleStructure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Elongation factor 4EF-4
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsRIBOSOME / ribosome elongation / GTPase EF4 / tRNA back-translocation / P-loop
Function / homology
Function and homology information


: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / ribosomal small subunit binding / misfolded RNA binding / transcription antitermination factor activity, RNA binding ...: / response to pH / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / ribosomal small subunit binding / 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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translation elongation factor activity / response to salt stress / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / response to cold / 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 / positive regulation of translation / 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 / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Ribosomal protein L1, bacterial-type / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site ...Elongation factor 4 / GTP-binding protein LepA, C-terminal / Elongation factor 4, domain IV / LepA, C-terminal domain superfamily / GTP-binding protein LepA C-terminus / Ribosomal protein L1, bacterial-type / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / 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 uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Elongation factor 4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang, D. / Yan, K. / Liu, G. / Song, G. / Luo, J. / Shi, Y. / Cheng, E. / Wu, S. / Jiang, T. / Low, J. ...Zhang, D. / Yan, K. / Liu, G. / Song, G. / Luo, J. / Shi, Y. / Cheng, E. / Wu, S. / Jiang, T. / Low, J. / Gao, N. / Qin, Y.
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome.
Authors: Dejiu Zhang / Kaige Yan / Guangqiao Liu / Guangtao Song / Jiejian Luo / Yi Shi / Erchao Cheng / Shan Wu / Taijiao Jiang / Jizhong Lou / Ning Gao / Yan Qin /
Abstract: EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2- ...EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Structure summary
Revision 1.3Feb 22, 2017Group: Database references
Revision 1.4Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: database_2 / em_image_scans ...database_2 / em_image_scans / entity / struct
Item: _entity.pdbx_description / _struct.pdbx_descriptor
Revision 1.5Dec 18, 2019Group: Advisory / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.6Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
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
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
5: 50S ribosomal protein L1
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 L11
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
x: Elongation factor 4
a: 16S ribosomal RNA
A: 23S ribosomal RNA
B: 5S ribosomal RNA
7: mRNA
8: tRNA
9: tRNA


Theoretical massNumber of molelcules
Total (without water)2,289,31057
Polymers2,289,31057
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0
#2: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V3
#3: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8
#4: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#5: Protein 30S ribosomal protein S6 / / 30S ribosomal protein S6 / fully modified isoform / 30S ribosomal protein S6 / non-modified isoform


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#6: Protein 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#7: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W7
#8: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7X3
#9: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5
#10: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#11: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsL / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3
#12: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S9
#13: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG59
#14: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#15: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T3
#16: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63
#17: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T7
#18: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U3
#19: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U7
#20: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: P68679

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50S ribosomal protein ... , 30 types, 30 molecules 012345CDEFGHIJKLMNOPQRSTUVWXYZ

#21: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmF, b1089, JW1075 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N4
#22: Protein 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmG / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N9
#23: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7P5
#24: Protein 50S ribosomal protein L35 /


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmI / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#25: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmJ, b3299, JW3261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q6
#26: Protein 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplA, b3984, JW3947 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L0
#27: Protein 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#28: Protein 50S ribosomal protein L3 /


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#29: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplD / Production host: Escherichia coli (E. coli) / References: UniProt: P60723
#30: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplE, b3308, JW3270 / Production host: Escherichia coli (E. coli) / References: UniProt: P62399
#31: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplF, b3305, JW3267 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG55
#32: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplI, b4203, JW4161 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1
#33: Protein 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplK, relC, b3983, JW3946 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7J7
#34: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplM, b3231, JW3200 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA10
#35: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplN, b3310, JW3272 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY3
#36: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplO, b3301, JW3263 / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#37: Protein 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#38: Protein 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplQ, b3294, JW3256 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG44
#39: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplR, b3304, JW3266 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C018
#40: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplS, b2606, JW2587 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7K6
#41: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L3
#42: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplU, b3186, JW3153 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG48
#43: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#44: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplW, b3318, JW3280 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#45: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplX, b3309, JW3271 / Production host: Escherichia coli (E. coli) / References: UniProt: P60624
#46: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rplY, b2185, JW2173 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919
#47: Protein 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#48: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmB, b3637, JW3612 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M2
#49: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmC, b3312, JW3274 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M6
#50: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpmD, b3302, JW3264 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG51

-
Protein , 1 types, 1 molecules x

#51: Protein Elongation factor 4 / EF-4 / EF-4 / Ribosomal back-translocase LepA


Mass: 66652.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: lepA, b2569, JW2553 / Production host: Escherichia coli (E. coli) / References: UniProt: P60785, EC: 3.6.5.1

-
RNA chain , 5 types, 6 molecules aAB789

#52: RNA chain 16S ribosomal RNA /


Mass: 496892.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#53: RNA chain 23S ribosomal RNA /


Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#54: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria)
#55: RNA chain mRNA / Messenger RNA


Mass: 4784.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: RNA chain tRNA / Transfer RNA


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-ID
1RECONSTRUCTION OF POST-EF4 COMPLEX.COMPLEX0
2EF41
3ribosome 70S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderTilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Num. of particles: 18772
Details: (SINGLE PARTICLE DETAILS: THE PARTICLES WERE SELECTED USING AN AUTOMATIC SELECTION PROGRAM.) (SINGLE PARTICLE- -APPLIED SYMMETRY: C1)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms46634 101181 0 0 147815

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