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- PDB-5afi: 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected ... -

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Basic information

Entry
Database: PDB / ID: 5afi
Title2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • A/T-site Phe-tRNAPhe
  • Elongation factor Tu 2EF-Tu
  • P-site fMet-tRNAfMet
  • mRNAMessenger RNA
KeywordsRIBOSOME / TRANSLATION / PROTEIN SYNTHESIS / DECODING / ELONGATION FACTOR TU / TRNA / RNA MODIFICATION / ANTIBIOTIC
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / translational elongation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing ...guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / translational elongation / stringent response / 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 / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / translation elongation factor activity / translational initiation / negative regulation of DNA-templated DNA replication 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 / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / molecular adaptor activity / rRNA binding / 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 / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Elongation factor Tu domain 2 / 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. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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
Similarity search - Domain/homology
N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / KIRROMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 ...N-FORMYLMETHIONINE / GUANOSINE-5'-DIPHOSPHATE / KIRROMYCIN / : / : / 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 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 uL29 / 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 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 / Elongation factor Tu 2 / Large ribosomal subunit protein uL2 / 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: 2.9 Å
AuthorsFischer, N. / Neumann, P. / Konevega, A.L. / Bock, L.V. / Ficner, R. / Rodnina, M.V. / Stark, H.
CitationJournal: Nature / Year: 2015
Title: Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.
Authors: Niels Fischer / Piotr Neumann / Andrey L Konevega / Lars V Bock / Ralf Ficner / Marina V Rodnina / Holger Stark /
Abstract: Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron ...Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.
History
DepositionJan 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Atomic model / Derived calculations
Revision 1.2Aug 2, 2017Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Aug 9, 2017Group: Structure summary / Category: audit_author / entity / Item: _audit_author.name / _entity.pdbx_description
Revision 2.0Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_database_proc / pdbx_seq_map_depositor_info / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.0Jun 26, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_seq_map_depositor_info
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2847
  • Imaged by UCSF Chimera
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Assembly

Deposited unit
a: 16S ribosomal RNA
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: P-site fMet-tRNAfMet
w: P-site fMet-tRNAfMet
x: mRNA
y: A/T-site Phe-tRNAPhe
z: Elongation factor Tu 2
A: 23S ribosomal RNA
B: 5S ribosomal RNA
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
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 L10
6: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,302,707401
Polymers2,292,94959
Non-polymers9,759342
Water37821
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1
MethodPISA

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Components

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RNA chain , 6 types, 7 molecules avwxyAB

#1: RNA chain 16S ribosomal RNA /


Mass: 498909.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: GenBank: 309700213
#22: RNA chain P-site fMet-tRNAfMet


Mass: 24818.893 Da / Num. of mol.: 2 / Fragment: Residues 49-125 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: GenBank: 147949
#23: RNA chain mRNA / Messenger RNA


Mass: 3492.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600
#24: RNA chain A/T-site Phe-tRNAPhe


Mass: 24797.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600
#26: RNA chain 23S ribosomal RNA /


Mass: 941521.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0CE48*PLUS
#27: RNA chain 5S ribosomal RNA /


Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600

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

#2: Protein 30S ribosomal protein S2 /


Mass: 26652.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7V0
#3: 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) / Variant: MRE 600 / References: UniProt: P0A7V3
#4: 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) / Variant: MRE 600 / References: UniProt: P0A7V8
#5: 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) / Variant: MRE 600 / References: UniProt: P0A7W1
#6: 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) / Variant: MRE 600 / References: UniProt: P02358
#7: 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) / Variant: MRE 600 / References: UniProt: P02359
#8: 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) / Variant: MRE 600 / References: UniProt: P0A7W7
#9: 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) / Variant: MRE 600 / References: UniProt: P0A7X3
#10: 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) / Variant: MRE 600 / References: UniProt: P0A7R5
#11: 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) / Variant: MRE 600 / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7S3
#13: 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) / Variant: MRE 600 / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14 /


Mass: 11677.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0AG59
#15: 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) / Variant: MRE 600 / References: UniProt: P0ADZ4
#16: 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) / Variant: MRE 600 / References: UniProt: P0A7T3
#17: 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) / Variant: MRE 600 / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7T7
#19: 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) / Variant: MRE 600 / References: UniProt: P0A7U3
#20: 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) / Variant: MRE 600 / References: UniProt: P0A7U7
#21: 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) / Variant: MRE 600 / References: UniProt: P68679

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Protein , 1 types, 1 molecules z

#25: Protein Elongation factor Tu 2 / EF-Tu / EF-Tu 2 / P-43


Mass: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0CE48

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

#28: 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) / Variant: MRE 600 / References: UniProt: P60422
#29: 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) / Variant: MRE 600 / References: UniProt: P60438, UniProt: P60422*PLUS
#30: 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) / Variant: MRE 600 / References: UniProt: P60723, UniProt: P60438*PLUS
#31: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P62399, UniProt: P60723*PLUS
#32: 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) / Variant: MRE 600 / References: UniProt: P0AG55, UniProt: P62399*PLUS
#33: 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) / Variant: MRE 600 / References: UniProt: P0A7R1, UniProt: P0AG55*PLUS
#34: 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) / Variant: MRE 600 / References: UniProt: P0A7J7, UniProt: P0A7R1*PLUS
#35: 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) / Variant: MRE 600 / References: UniProt: P0AA10, UniProt: P0A7J7*PLUS
#36: 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) / Variant: MRE 600 / References: UniProt: P0ADY3, UniProt: P0AA10*PLUS
#37: 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) / Variant: MRE 600 / References: UniProt: P02413, UniProt: P0ADY3*PLUS
#38: 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) / Variant: MRE 600 / References: UniProt: P0ADY7, UniProt: P02413*PLUS
#39: 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) / Variant: MRE 600 / References: UniProt: P0AG44, UniProt: P0ADY7*PLUS
#40: 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) / Variant: MRE 600 / References: UniProt: P0C018, UniProt: P0AG44*PLUS
#41: 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) / Variant: MRE 600 / References: UniProt: P0A7K6, UniProt: P0C018*PLUS
#42: 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) / Variant: MRE 600 / References: UniProt: P0A7L3, UniProt: P0A7K6*PLUS
#43: 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) / Variant: MRE 600 / References: UniProt: P0AG48, UniProt: P0A7L3*PLUS
#44: 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) / Variant: MRE 600 / References: UniProt: P61175, UniProt: P0AG48*PLUS
#45: 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) / Variant: MRE 600 / References: UniProt: P0ADZ0, UniProt: P61175*PLUS
#46: 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) / Variant: MRE 600 / References: UniProt: P60624, UniProt: P0ADZ0*PLUS
#47: 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) / Variant: MRE 600 / References: UniProt: P68919, UniProt: P60624*PLUS
#48: 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) / Variant: MRE 600 / References: UniProt: P0A7L8, UniProt: P68919*PLUS
#49: 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) / Variant: MRE 600 / References: UniProt: P0A7M2, UniProt: P0A7L8*PLUS
#50: 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) / Variant: MRE 600 / References: UniProt: P0A7M6, UniProt: P0A7M2*PLUS
#51: 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) / Variant: MRE 600 / References: UniProt: P0AG51, UniProt: P0A7M6*PLUS
#52: 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) / Variant: MRE 600 / References: UniProt: P0A7N4, UniProt: P0AG51*PLUS
#53: Protein 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7N9, UniProt: P0A7N4*PLUS
#54: 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) / Variant: MRE 600 / References: UniProt: P0A7P5, UniProt: P0A7N9*PLUS
#55: Protein 50S ribosomal protein L35 / / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7Q1, UniProt: P0A7P5*PLUS
#56: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7Q6, UniProt: P0A7Q1*PLUS
#57: Protein 50S ribosomal protein L10 / / 50S ribosomal protein L8


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600 / References: UniProt: P0A7J3, UniProt: P0A7Q6*PLUS
#58: 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) / Variant: MRE 600 / References: UniProt: P0A7M9, UniProt: P0A7J3*PLUS

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Non-polymers , 8 types, 363 molecules

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


Mass: 24.305 Da / Num. of mol.: 333 / Source method: obtained synthetically / Formula: Mg / References: UniProt: P0A7M9*PLUS
#60: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#61: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H11NO3S / Source: (natural) Escherichia coli (E. coli) / Variant: MRE 600
#62: Chemical ChemComp-KIR / KIRROMYCIN / MOCIMYCIN / DELVOMYCIN / MYC-8003


Mass: 796.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H60N2O12
#63: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#64: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#65: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 21 / 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

ComponentName: E. COLI 70S-EF-TU-GDP- KIRROMYCIN-PHE-TRNAPHE- FMET-TRNAFMET-TRNAFMET COMPLEX
Type: RIBOSOME
Buffer solutionName: 50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN
pH: 7.5
Details: 50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUIDE ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 20, 2011
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 192000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Custom3D reconstruction
2IMAGIC53D reconstruction
3RELION1.23D reconstruction
CTF correctionDetails: LOCAL CTF CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Num. of particles: 417201 / Actual pixel size: 0.75525 Å
Magnification calibration: CROSS- -CORRELATION WITH PUBLISHED ATOMIC COORDINATES
Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementHighest resolution: 2.9 Å

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