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- EMDB-6934: Ribosome Structure bound to ABC-F protein. -

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Basic information

Entry
Database: EMDB / ID: 6934
TitleRibosome Structure bound to ABC-F protein.
Map data
SampleBacterial ribosome in complex with MsrE:
(nucleic-acidNucleic acid) x 5 / (30S ribosomal protein ...) x 20 / (50S ribosomal protein ...) x 30 / Macrolide efflux protein / (ligand) x 2
Function / homologyL28p-like / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S11 superfamily ...L28p-like / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L10e/L16 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S3, C-terminal domain / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L25, C-terminal / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / ABC transporter / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L35 superfamily / L21-like superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L3 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L1, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S14, type Z / Ribosomal protein L10 / Ribosomal protein S7 domain / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L1-like / Ribosomal protein S16 domain superfamily / Ribosomal protein S6 superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / Ribosomal protein L35 signature. / ABC-transporter extension domain / 30S ribosomal protein Thx / Ribosomal protein L5, N-terminal / Ribosomal protein L15 / P-loop containing nucleoside triphosphate hydrolase / 30S ribosomal protein / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L31 type A / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L34, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein L14 signature. / Ribosomal protein L11 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / 30S ribosomal protein Thx / Ribosomal protein TL5, C-terminal domain / ABC transporter / KH domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L5 signature. / Ribosomal protein S9 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein L33 signature. / Ribosomal protein L34 signature. / Ribosomal protein L13 signature. / Ribosomal protein S13 signature. / Ribosomal protein L30 signature. / Ribosomal protein S4 signature. / Ribosomal protein S5 signature.
Function and homology information
SourceThermus thermophilus (bacteria) / Thermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSu WX / Kumar V / Ero R / Andrew SWW / Jian S / Yong-Gui G
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ribosome protection by antibiotic resistance ATP-binding cassette protein.
Authors: Weixin Su / Veerendra Kumar / Yichen Ding / Rya Ero / Aida Serra / Benjamin Sian Teck Lee / Andrew See Weng Wong / Jian Shi / Siu Kwan Sze / Liang Yang / Yong-Gui Gao
Abstract: The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer ...The ribosome is one of the richest targets for antibiotics. Unfortunately, antibiotic resistance is an urgent issue in clinical practice. Several ATP-binding cassette family proteins confer resistance to ribosome-targeting antibiotics through a yet unknown mechanism. Among them, MsrE has been implicated in macrolide resistance. Here, we report the cryo-EM structure of ATP form MsrE bound to the ribosome. Unlike previously characterized ribosomal protection proteins, MsrE is shown to bind to ribosomal exit site. Our structure reveals that the domain linker forms a unique needle-like arrangement with two crossed helices connected by an extended loop projecting into the peptidyl-transferase center and the nascent peptide exit tunnel, where numerous antibiotics bind. In combination with biochemical assays, our structure provides insight into how MsrE binding leads to conformational changes, which results in the release of the drug. This mechanism appears to be universal for the ABC-F type ribosome protection proteins.
Validation ReportPDB-ID: 5zlu

SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Aug 1, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5zlu
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6934.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.1 Å/pix.
= 396. Å
360 pix
1.1 Å/pix.
= 396. Å
360 pix
1.1 Å/pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.052 (by author), 0.08 (movie #1):
Minimum - Maximum-0.339491 - 0.56833124
Average (Standard dev.)0.00219343 (0.020815672)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.3390.5680.002

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Supplemental data

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Sample components

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Entire Bacterial ribosome in complex with MsrE

EntireName: Bacterial ribosome in complex with MsrE / Number of components: 59

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Component #1: protein, Bacterial ribosome in complex with MsrE

ProteinName: Bacterial ribosome in complex with MsrE / Recombinant expression: No
MassTheoretical: 2.8 MDa
SourceSpecies: Thermus thermophilus (bacteria) / Strain: HB8

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Component #2: nucleic-acid, RNA (25-mer)

Nucleic-acidName: RNA (25-mer) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCAAGGAGG UAAAAAUGUU CAAAA
MassTheoretical: 8.15698 kDa
SourceSpecies: Thermus thermophilus HB8 (bacteria)

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Component #3: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.193475 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #4: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.483172 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #5: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.736143 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #6: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.605464 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #7: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.954968 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #8: protein, 30S ribosomal protein Thx

ProteinName: 30S ribosomal protein ThxRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.35003 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #9: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGGAGAGUUU GAUCCUGGCU CAGGGUGAAC GCUGGCGGCG UGCCUAAGAC AUGCAAGUCG UGCGGGCCGC GGGGUUUUAC UCCGUGGUCA GCGGCGGACG GGUGAGUAAC GCGUGGGUGA CCUACCCGGA AGAGGGGGAC AACCCGGGGA AACUCGGGCU AAUCCCCCAU GUGGACCCGC CCCUUGGGGU GUGUCCAAAG GGCUUUGCCC GCUUCCGGAU GGGCCCGCGU CCCAUCAGCU AGUUGGUGGG GUAAUGGCCC ACCAAGGCGA CGACGGGUAG CCGGUCUGAG AGGAUGGCCG GCCACAGGGG CACUGAGACA CGGGCCCCAC UCCUACGGGA GGCAGCAGUU AGGAAUCUUC CGCAAUGGGC GCAAGCCUGA CGGAGCGACG CCGCUUGGAG GAAGAAGCCC UUCGGGGUGU AAACUCCUGA ACCCGGGACG AAACCCCCGA CGAGGGGACU GACGGUACCG GGGUAAUAGC GCCGGCCAAC UCCGUGCCAG CAGCCGCGGU AAUACGGAGG GCGCGAGCGU UACCCGGAUU CACUGGGCGU AAAGGGCGUG UAGGCGGCCU GGGGCGUCCC AUGUGAAAGA CCACGGCUCA ACCGUGGGGG AGCGUGGGAU ACGCUCAGGC UAGACGGUGG GAGAGGGUGG UGGAAUUCCC GGAGUAGCGG UGAAAUGCGC AGAUACCGGG AGGAACGCCG AUGGCGAAGG CAGCCACCUG GUCCACCCGU GACGCUGAGG CGCGAAAGCG UGGGGAGCAA ACCGGAUUAG AUACCCGGGU AGUCCACGCC CUAAACGAUG CGCGCUAGGU CUCUGGGUCU CCUGGGGGCC GAAGCUAACG CGUUAAGCGC GCCGCCUGGG GAGUACGGCC GCAAGGCUGA AACUCAAAGG AAUUGACGGG GGCCCGCACA AGCGGUGGAG CAUGUGGUUU AAUUCGAAGC AACGCGAAGA ACCUUACCAG GCCUUGACAU GCUAGGGAAC CCGGGUGAAA GCCUGGGGUG CCCGCGAGGG GAGCCCUAGC ACAGGUGCUG CAUGGCCGUC GUCAGCUCGU GCCGUGAGGU GUUGGGUUAA GUCCCGCAAC GAGCGCAACC CCCGCCGUUA GUUGCCAGCG GUUCGGCCGG GCACUCUAAC GGGACUGCCC GCGAAAGCGG GAGGAAGGAG GGGACGACGU CUGGUCAGCA UGGCCCUUAC GGCCUGGGCG ACACACGUGC UACAAUGCCC ACUACAAAGC GAUGCCACCC GGCAACGGGG AGCUAAUCGC AAAAAGGUGG GCCCAGUUCG GAUUGGGGUC UGCAACCCGA CCCCAUGAAG CCGGAAUCGC UAGUAAUCGC GGAUCAGCCA UGCCGCGGUG AAUACGUUCC CGGGCCUUGU ACACACCGCC CGUCACGCCA UGGGAGCGGG CUCUACCCGA AGUCGCCGGG AGCCUACGGG CAGGCGCCGA GGGUAGGGCC CGUGACUGGG GCGAAGUCGU AACAAGGUAG CUGUACCGGA AGGUGCGGCU GGAUCACCUC CUUU
MassTheoretical: 491.471938 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #10: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.317703 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #11: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.751076 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #12: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.373447 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #13: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.583416 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #14: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.988753 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #15: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.050973 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #16: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.86857 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #17: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.410614 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #18: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.737868 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #19: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.637384 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #20: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.338861 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #21: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.158725 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #22: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.578407 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #23: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.409983 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #24: nucleic-acid, 23S ribosomal RNA

Nucleic-acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAGAUGGUAA GGGCCCACGG UGGAUGCCUC GGCACCCGAG CCGAUGAAGG ACGUGGCUAC CUGCGAUAAG CCAGGGGGAG CCGGUAGCGG GCGUGGAUCC CUGGAUGUCC GAAUGGGGGA ACCCGGCCGG CGGGAAGCCG GUCACCGCGC UUUUGCGCGG GGGGAACCUG GGGAACUGAA ACAUCUCAGU ACCCAGAGGA GAGGAAAGAG AAAUCGACUC CCUGAGUAGC GGCGAGCGAA AGGGGACCAG CCUAAACCGU CCGGCUUGUC CGGGCGGGGU CGUGGGGCCC UCGGACACCG AAUCCCCAGC CUAGCCGAAG CUGUUGGGAA GCAGCGCCAG AGAGGGUGAA AGCCCCGUAG GCGAAAGGUG GGGGGAUAGG UAGGGUGCCC GAGUACCCCG UGGUUCGUGG AGCCAUGGGG GAAUCUGGGC GGACCACCGC CUAAGGCUAA GUACUCCGGG UGACCGAUAG CGCACCAGUA CCGUGAGGGA AAGGUGAAAA GAACCCCGGG AGGGGAGUGA AAUAGAGCCU GAAACCGUGG GCUUACAAGC AGUCACGGCC CCGCAAGGGG UUGUGGCGUG CCUAUUGAAG CAUGAGCCGG CGACUCACGG UCGUGGGCGA GCUUAACCGU UGAGCGGAGG CGUAGGGAAA CCGAGUCCGA ACAGGGCGCA AAGUCCGCGG CCGUGGACCC GAAACCGGGC GAGCUAGCCC UGGCCAGGGU GAAGCUGGGG UGAGACCCAG UGGAGGCCCG AACCGGUGGG GGAUGCAAAC CCCUCGGAUG AGCUGGGGCU AGGAGUGAAA AGCUAACCGA GCCCGGAGAU AGCUGGUUCU CCCCGAAAUG ACUUUAGGGU CAGCCUCAGG CGCUGACUGG GGCCUGUAGA GCACUGAUAG GGCUAGGGGG CCCACCAGCC UACCAAACCC UGUCAAACUC CGAAGGGUCC CAGGUGGAGC CUGGGAGUGA GGGCGCGAGC GAUAACGUCC GCGUCCGAGC GCGGGAACAA CCGAGACCGC CAGCUAAGGC CCCCAAGUCU GGGCUAAGUG GUAAAGGAUG UGGCGCCGCG AAGACAGCCA GGAGGUUGGC UUAGAAGCAG CCAUCCUUUA AAGAGUGCGU AAUAGCUCAC UGGUCGAGUG GCGCCGCGCC GAAAAUGAUG CGGGGCUUAA GCCCAGCGCC GAAGCUGCGG GUCUGGGGGA UGACCCCAGG CGGUAGGGGA GCGUUCCCGA UGCCGAUGAA GGCCGACCCG CGAGGCGGCU GGAGGUAAGG GAAGUGCGAA UGCCGGCAUG AGUAACGAUA AAGAGGGUGA GAAUCCCUCU CGCCGUAAGC CCAAGGGUUC CUACGCAAUG GUCGUCAGCG UAGGGUUAGG CGGGACCUAA GGUGAAGCCG AAAGGCGUAG CCGAAGGGCA GCCGGUUAAU AUUCCGGCCC UUCCCGCAGG UGCGAUGGGG GGACGCUCUA GGCUAGGGGG ACCGGAGCCA AUGGACGAGC CCGGCCAGAA GCGCAGGGUG GGAGGUAGGC AAAUCCGCCU CCCAACAAGC UCUGCGUGGU GGGGAAGCCC GUACGGGUGA CAACCCCCCG AAGCCAGGGA GCCAAGAAAA GCCUCUAAGC ACAACCUGCG GGAACCCGUA CCGCAAACCG ACACAGGUGG GCGGGUGCAA GAGCACUCAG GCGCGCGGGA GAACCCUCGC CAAGGAACUC UGCAAGUUGG CCCCGUAACU UCGGGAGAAG GGGUGCUCCC UGGGGUGAUG AGCCCCGGGA GCCGCAGUGA ACAGGCUCUG GCGACUGUUU ACCAAAAACA CAGCUCUCUG CGAACUCGUA AGAGGAGGUA UAGGGAGCGA CGCUUGCCCG GUGCCGGAAG GUCAAGGGGA GGGGUGCAAG CCCCGAACCG AAGCCCCGGU GAACGGCGGC CGUAACUAUA ACGGUCCUAA GGUAGCGAAA UUCCUUGUCG GGUAAGUUCC GACCUGCACG AAAAGCGUAA CGACCGGAGC GCUGUCUCGG CGAGGGACCC GGUGAAAUUG AACUGGCCGU GAAGAUGCGG CCUACCCGUG GCAGGACGAA AAGACCCCGU GGAGCUUUAC UGCAGCCUGG UGUUGGCUCU UGGUCGCGCC UGCGUAGGAU AGGUGGGAGC CUGUGAACCC CCGCCUCCGG GUGGGGGGGA GGCGCCGGUG AAAUACCACC CUGGCGCGGC UGGGGGCCUA ACCCUCGGAU GGGGGGACAG CGCUUGGCGG GCAGUUUGAC UGGGGCGGUC GCCUCCUAAA AGGUAACGGA GGCGCCCAAA GGUCCCCUCA GGCGGGACGG AAAUCCGCCG GAGAGCGCAA GGGUAGAAGG GGGCCUGACU GCGAGGCCUG CAAGCCGAGC AGGGGCGAAA GCCGGGCCUA GUGAACCGGU GGUCCCGUGU GGAAGGGCCA UCGAUCAACG GAUAAAAGUU ACCCCGGGGA UAACAGGCUG AUCUCCCCCG AGCGUCCACA GCGGCGGGGA GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GAAGAAGGUC CCAAGGGUUG GGCUGUUCGC CCAUUAAAGC GGCACGCGAG CUGGGUUCAG AACGUCGUGA GACAGUUCGG UCUCUAUCCG CCACGGGCGC AGGAGGCUUG AGGGGGGCUC UUCCUAGUAC GAGAGGACCG GAAGGGACGC ACCUCUGGUU UCCCAGCUGU CCCUCCAGGG GCAUAAGCUG GGUAGCCAUG UGCGGAAGGG AUAACCGCUG AAAGCAUCUA AGCGGGAAGC CCGCCCCAAG AUGAGGCCUC CACGGCGUCA AGCCGGAAGG ACCCGGGAAG ACCACCCGGU GGAUGGGCCG GGGGUGUAAG CGCCGCGAGG CGUUGAGCCG ACCGGUCCCA AUCGUCCGAG GUCUU
MassTheoretical: 935.028375 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #25: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAUCCCCCGU GCCCAUAGCG GCGUGGAACC ACCCGUUCCC AUUCCGAACA CGGAAGUGAA ACGCGCCAGC GCCGAUGGUA CUGGGCGGGC GACCGCCUGG GAGAGUAGGU CGGUGCGGGG GAU
MassTheoretical: 39.846781 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #26: protein, 50S ribosomal protein L1

ProteinName: 50S ribosomal protein L1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.867699 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #27: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.532551 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #28: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.450213 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #29: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.271914 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #30: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.061596 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #31: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.568926 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #32: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.586639 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #33: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.526111 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #34: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.927903 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #35: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.309586 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #36: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.319142 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #37: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.993909 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #38: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.750148 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #39: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.639845 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #40: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.18883 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #41: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.779275 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #42: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.069153 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #43: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.808055 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #44: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.759808 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #45: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.085611 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #46: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.238572 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #47: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.529074 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #48: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.112597 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #49: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.799126 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #50: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.300543 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #51: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.72205 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #52: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.632896 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #53: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.132449 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #54: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.506178 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #55: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.435411 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

+
Component #56: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGG(4SU)GG AGCAGCCCGG UAGCUCGUCG GG(OMC)ACAUAAC CCGAAG(7MG)UCG UCGG(5MU)(PSU)CAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.885 kDa
SourceSpecies: Thermus thermophilus HB8 (bacteria)

+
Component #57: protein, Macrolide efflux protein

ProteinName: Macrolide efflux protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.706461 kDa
SourceSpecies: Pseudomonas aeruginosa (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #58: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #59: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 127778
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
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