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- EMDB-10809: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-10809
TitleAcinetobacter baumannii ribosome-amikacin complex - 50S subunit
Map dataAcinetobacter baumannii ribosome-amikacin complex - 50S subunit, post-processed map
Sample
  • Complex: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
    • RNA: x 3 types
    • Protein or peptide: x 27 types
  • Ligand: x 2 types
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 ...Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / 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 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 L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / ribosomal L5P family C-terminus / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif.
Similarity search - Domain/homology
50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L28 / 50S ribosomal protein L33 / 50S ribosomal protein L19 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 ...50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L28 / 50S ribosomal protein L33 / 50S ribosomal protein L19 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L34 / 50S ribosomal protein L13
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNicholson D / Edwards TA / O'Neill AJ / Ranson NA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust203743/Z/16/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Authors: David Nicholson / Thomas A Edwards / Alex J O'Neill / Neil A Ranson /
Abstract: Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and ...Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii.
History
DepositionMar 30, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yhs
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10809.png

Downloads & links

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Map

FileDownload / File: emd_10809.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 50S subunit, post-processed map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.1510258 - 0.34048384
Average (Standard dev.)0.00025076594 (±0.0062989923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.000428.000428.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1510.3400.000

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Supplemental data

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Mask #1

Fileemd_10809_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Acinetobacter baumannii ribosome-amikacin complex, consensus map filtered by...

Fileemd_10809_additional.map
AnnotationAcinetobacter baumannii ribosome-amikacin complex, consensus map filtered by local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half...

Fileemd_10809_half_map_1.map
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 50S subunit, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit, half...

Fileemd_10809_half_map_2.map
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 50S subunit, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Acinetobacter baumannii ribosome-amikacin complex - 50S subunit

EntireName: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
Components
  • Complex: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • RNA: E-site tRNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit

SupramoleculeName: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Macromolecule #1: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 940.330125 KDa
SequenceString: AGUCAAGUAA UUAAGUGCAU GUGGUGGAUG CCUUGGCAGU CAGAGGCGAU GAAAGACGUG AUAGCCUGCG AAAAGCUCCG GGGAGGCGG CAAAUAUCCU UUGAUCCGGA GAUGUCUGAA UGGGGGAACC CACCUACUUU AAGGUAGGUA UUGCAACAUG A AUACAUAG ...String:
AGUCAAGUAA UUAAGUGCAU GUGGUGGAUG CCUUGGCAGU CAGAGGCGAU GAAAGACGUG AUAGCCUGCG AAAAGCUCCG GGGAGGCGG CAAAUAUCCU UUGAUCCGGA GAUGUCUGAA UGGGGGAACC CACCUACUUU AAGGUAGGUA UUGCAACAUG A AUACAUAG UGUUGCAAGG CGAACGAGGG GAAGUGAAAC AUCUCAGUAC CCUUAGGAAA AGAAAUCAAU UGAGAUUCCC UC AGUAGCG GCGAGCGAAC GGGGAUCAGC CCAUUAAGUU AUGUGUGUUU UAGUGGAACG CUCUGGGAAG UGCGAACGUA GAG GGUGAU AUUCCCGUAC ACGAAAGGGC ACACAUAAUG AUGACGAGUA GGGCGAGGCA CGUGAAACCU UGUCUGAAUA UGGG GGGAC CAUCCUCCAA GGCUAAAUAC UCCUGACUGA CCGAUAGUGA ACCAGUACCG UGAGGGAAAG GCGAAAAGAA CCCCU GUGA GGGGAGUGAA AUAGAUCCUG AAACCGCAUG CAUACAAGCA GUGGGAGCAC CUUUGUGGUG UGACUGCGUA CCUUUU GUA UAAUGGGUCA GCGACUUAUA UUCAGUAGCG AGGUUAACCG UAUAGGGGAG CCGUAGAGAA AUCGAGUCUU AAUAGGG CG UUUAGUUGCU GGGUAUAGAC CCGAAACCAG GCGAUCUAUC CAUGAGCAGG UUGAAGGUUG GGUAACACUA ACUGGAGG A CCGAACCCAC UGUCGUUGAA AAGCCAGGGG AUGACUUGUG GAUAGGGGUG AAAGGCUAAU CAAGCCUGGU GAUAGCUGG UUCUCCCCGA AAGCUAUUUA GGUAGCGCCU CGGACGAAUA CCAUAGGGGG UAGAGCACUG UUUCGGCUAG GGGGUCAUCC CGACUUACC AAACCGAUGC AAACUCCGAA UACCUAUGAG UACUAUCCGG GAGACAGACU GCGGGUGCUA ACGUCCGUAG U CAAGAGGA AAACAAUCCA GACCGCCAGC UAAGGCCCCA AAAUCAUAGU UAAGUGGGAA ACGAUGUGGG AAGGCAUAGA CA GCUAGGA GGUUGGCUUA GAAGCAGCCA CCCUUUAAAG AAAGCGUAAU AGCUCACUAG UCGAGUCGGC CUGCGCGGAA GAU GUAACG GGGCUAAAAC UAUGUGCCGA AGCUGCGGAU GUAUACUUUG UAUACGUGGU AGGGGAGCGU UCUGUAAGCC GAUG AAGGU GUGUUGAGAA GCAUGCUGGA GGUAUCAGAA GUGCGAAUGC UGACGUGAGU AACGACAAAA CGGGUGAAAA ACCCG UUCG CCGAAAGACC AAGGGUUCCA GUCCAACGUU AAUCGGGGCU GGGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGU AGU CGAUGGGAAA AUGGUUAAUA UUCCAUUACU UCUGUGUAAU GCGAUGAGAG GACGGAGAAG GCUAAAUCAG CCUGGCG UU GGUUGUCCAG GUGAAAGGAU GUAGGCAUGU AUCUUAGGCA AAUCCGGGGU ACUCUAUGCU GAGAUCUGAU AGCAAGCU G UACUUGUACA GCGAAGUGGU UGAUGCCAUG CUUCCAGGAA AAGUCUCUAA GCUUCAGUUA CACAGGAAUC GUACCCGAA ACCGACACAG GUGGUCAGGU CGAGUAGACC AAGGCGCUUG AGAGAACUCU GCUGAAGGAA CUAGGCAAAA UGGUACCGUA ACUUCGGGA GAAGGUACGC UGUUGUUGGU GAUGGAACUC GCUUCCUGAG CUGACGACAG CCGCAGAAAC CAGGCCGCUG C AACUGUUU AUUAAAAACA UAGCACUCUG CAAACACGAA AGUGGACGUA UAGGGUGUGA UGCCUGCCCG GUGCUGGAAG GU UAAUUGA UGGGGUUAGC GUAAGCGAAG CUCUUGAUCG AAGCCCCAGU AAACGGCGGC CGUAACUAUA ACGGUCCUAA GGU AGCGAA AUUCCUUGUC GGGUAAGUUC CGACCUGCAC GAAUGGCAUA AUGAUGGCGG CGCUGUCUCC AGCAGAGGCU CAGU GAAAU CGAAAUCGCU GUGAAGAUGC AGUGUACCCG CGGCUAGACG GAAAGACCCC GUGAACCUUU ACUGCAGCUU GACAC UGAA CUUUGACCUU ACUUGUGUAG GAUAGGUGGG AGGCUUUGAA GCUGGAACGC UAGUUCCAGU GGAGCCGUCC UUGAAA UAC CACCCUGGUA AUGUUGAGGU UCUAACUCUG UCCCGUGAUC CGGGACGAGG ACCGUGUCUG GUGGGUAGUU UGACUGG GG CGGUCUCCUC CUAAAGAGUA ACGGAGGAGU ACGAAGGUGC GCUCAGCGUG GUCGGAAAUC ACGCGUAGAG UAUAAAGG C AAAAGCGCGC UUAACUGCGA GACCCACAAG UCGAGCAGGU ACGAAAGUAG GUCUUAGUGA UCCGGUGGUU CUGUAUGGA AGGGCCAUCG CUCAACGGAU AAAAGGUACU CUGGGGAUAA CAGGCUGAUA CCGCCCAAGA GUUCAUAUCG ACGGCGGUGU UUGGCACCU CGAUGUCGGC UCAUCUCAUC CUGGGGCUGA AGCAGGUCCC AAGGGUAUGG CUGUUCGCCA UUUAAAGAGG U ACGCGAGC UGGGUUUAGA ACGUCGUGAG ACAGUUCGGU CCCUAUCUAC CGUGGGCGCU GGAAAUUUGA GAGGAUCUGC UC CUAGUAC GAGAGGACCA GAGUGGACGA ACCUCUGGUG UACCGGUUGU GACGCCAGUC GCAUCGCCGG GUAGCUAUGU UCG GAAGGG AUAACCGCUG AAAGCAUCUA AGCGGGAAGC CUACCUCAAG AUAAGAUUUC CCUAGGACUU UAUGUCCUCU AAAG AGCCG UUCGAGACUA GGACGUUGAU AGGUUGGAUG UGGAAGCAUA GUGAUAUGUG AAGCUGACCA AUACUAAUUG CUCGU GAGG CUUGACUAUA CAACACCCA

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Macromolecule #2: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 37.608344 KDa
SequenceString:
UGCUGGCGAC CAUAGCAAGA GUGAACCACC UGAUCCCUUC CCGAACUCAG AAGUGAAACC UCUUAGCGCU GAUGGUAGUG UGGGAUUAC CCAUGUGAGA GUAAGUCAUC GCCAGCUC

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Macromolecule #3: E-site tRNA

MacromoleculeName: E-site tRNA / type: rna / ID: 3
Details: E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs
Number of copies: 2
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 24.346498 KDa
SequenceString:
CGCGGGG(N)GG AGCAGCCUGG (N)AGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGG(N)(N)CAAA UCCGGCCCCC GC AACCA

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Macromolecule #4: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 30.319092 KDa
SequenceString: MPIQKCKPTS PGRRFVEKVV HDHLHKGAPY APLVEAKKRT GGRNNNGHIT TRHVGGGHKQ HYRIVDFKRN KDGVPAVVER IEYDPSRTA HIALLKYADG ERRYIIAPKG LRAGDKVQSG NDAPIRPGNC LPLRNMPIGS TLHNVELKIG KGAQLARSAG A SVQLLGRD ...String:
MPIQKCKPTS PGRRFVEKVV HDHLHKGAPY APLVEAKKRT GGRNNNGHIT TRHVGGGHKQ HYRIVDFKRN KDGVPAVVER IEYDPSRTA HIALLKYADG ERRYIIAPKG LRAGDKVQSG NDAPIRPGNC LPLRNMPIGS TLHNVELKIG KGAQLARSAG A SVQLLGRD GSYAIIRLRS GEMRKVHVEC RAVIGEVSNQ ENNLRSLGKA GAARWRGVRP TVRGMAMNPI DHPHGGGEGR NK GIQPVSP WGQKAKGYKT RTNKRTTKMI IRDRRVK

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Macromolecule #5: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 22.512639 KDa
SequenceString: MAIGLVGRKC GMTRIFTDAG VSVPVTVIEV DPNRITQIKT LETDGYQAVQ VTTGERRESR VTNAQKGHFA KAGVAAGRLV KEFRVTEAE LEGREVGGTI GVDLFTVGQI VDVTGQSKGK GFQGGVKRWN FRTQDATHGN SVSHRVLGST GQNQTPGRVF K GKKMAGHL ...String:
MAIGLVGRKC GMTRIFTDAG VSVPVTVIEV DPNRITQIKT LETDGYQAVQ VTTGERRESR VTNAQKGHFA KAGVAAGRLV KEFRVTEAE LEGREVGGTI GVDLFTVGQI VDVTGQSKGK GFQGGVKRWN FRTQDATHGN SVSHRVLGST GQNQTPGRVF K GKKMAGHL GDERVTVQGL EIVSVDTERS VLVVKGAIPG ATGGDVIVRP TIKA

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Macromolecule #6: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 6 / Details: residues 2-12 modelled without side chains / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 21.583904 KDa
SequenceString: MNLKTVSGSA VELSEVAFGR EFNEALVHQV VTAYLAGGRQ GTRAHKSRAD VSGGGKKPFR QKGTGRARAG SIRSPIWVGG GKTFAARPQ DWSQKVNRKM YRGAMQCILA ELVRQDRLVL VEEFAVAAPK TKELLAKLND LNAARALIVT DAVDENLYLA A RNLPHVDV ...String:
MNLKTVSGSA VELSEVAFGR EFNEALVHQV VTAYLAGGRQ GTRAHKSRAD VSGGGKKPFR QKGTGRARAG SIRSPIWVGG GKTFAARPQ DWSQKVNRKM YRGAMQCILA ELVRQDRLVL VEEFAVAAPK TKELLAKLND LNAARALIVT DAVDENLYLA A RNLPHVDV VDATAIDPVS LIAFDKVVMS VAAAKKIEVE LG

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Macromolecule #7: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 7 / Details: modelled without side chains / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 20.051471 KDa
SequenceString:
MARLKARYND ELKAKLQEEL SIKNVMEIPR ITKITLNMGV GAAATDKKLL DGAVADMQLI AGQKPVVTLA RKSIAGFKIR DGWPIGCKV TLRGDQMYEF LDRLISIAIP RIRDFRGFSA KSFDGRGNYS MGLKEQIVFP EIDFDKIDRI RGMDITITTT A RTDDEGRA LMRAFGFPFK

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Macromolecule #8: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 19.126047 KDa
SequenceString:
MSRVAKAPVT VPNGVTVTQN GRQVEVKGSK GTLSFNLHAL VELKQEEGKL QLAPAKESKD AWMQAGTARA VLNNLVKGVS EGFERKLQL VGVGYKAAVK GTVVNLNLGY SHPIDYALPE GVTAETPTAT EIILKSANKQ LLGQVAAEIR AYRSPEPYKG K GVRYSDEV ILRKEAKKK

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Macromolecule #9: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 15.95144 KDa
SequenceString:
MKTLSAKPAE VQHDWFVVDA TGKTLGRLAT EIARRLRGKH KTSYTPHVDA GDYIIVINAE QVQVTGNKAL DKKYYRHTEF PGGLKETNF EKLVAHKPEE IFERAVKGML PKGPLGYAMI KKMKVYAGSE HPHAAQQPQV LDI

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Macromolecule #10: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 13.523863 KDa
SequenceString:
MIQTETMLDV ADNSGARRVQ CIKVLGGSHR RYASVGDIIK VTVKEAIPRA RVKKGDVMNA VVVRTKFGIR RPDGSVIRFD DNAAVILNN NKAPIATRIF GPVTRELRTE QFMKIISLAP EVL

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Macromolecule #11: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 15.509915 KDa
SequenceString:
MTLRLNELAP AEGAKREHRR LGRGIGSGVG KTGGRGIKGQ KSRKSGGVRP GFEGGQTAIY RRLPKFGFTS QIALKTAEVR LSELSKVEG DIVSLETLKA ANVVRRDQIR ARIVLSGEIT RAFTVQGVAL TKGAKAAIEA AGGKVEE

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Macromolecule #12: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 15.498312 KDa
SequenceString:
MLQPKRTKFR KVHKGRNTGL AHRGSTVSFG SIAIKATERG RMTARQIEAA RRTISRRIKR GGKIFIRVFP DKPITEKPLE VRMGNGKGN VEYWVCEIKP GKILYEIEGV NEDLAREAFA LAAAKLPFKT TIVTRTVM

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Macromolecule #13: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 14.02123 KDa
SequenceString:
MRHRNSGVKL GRTSSHRKAM FQNLANSLFE HELIKTTLPK AKELRRVAEP LITLAKNDTV ANRRLAFART RNAATVGKLF TVLGPRYKE RNGGYLRVLK AGFRAGDAAP MAYVELVDRE VNTSAE

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Macromolecule #14: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 12.443341 KDa
SequenceString:
MNEKKQSRLR RAKSTRLHIR ALGATRLCVN RTPRHIYAQV ISADGGKVLA QASTLDASLR SGTTGNIEAA TKVGALIAER AKAAGVTKV AFDRSGFKYH GRIKALADAA REGGLEF

+
Macromolecule #15: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 13.619865 KDa
SequenceString:
MSGKHPLVQA IENSQLKTDL PEFAPGDTVV VQVKVKEGDR ERLQAFEGVV IAKKNRGLNS AFTVRKISSG VGVERVFQTH SPVVAKIEV KRRGDVRRAK LYYLRDLSGK AARIREKLPA RKA

+
Macromolecule #16: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 13.468946 KDa
SequenceString:
MARVKRGVVA HRRHKKILAR AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQKKRQFRAL WIARINAGAR QNGLSYSRMI DGLKKAQVI IDRRVLADIA MHDAVAFAAL AEKAKGALAA

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Macromolecule #17: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 11.496364 KDa
SequenceString:
MYAVIQSGGK QHRVVEGETL KVELLKAESG ATITFDDVLM VVNGDNIQIG APVVAGAKVT AEVIGHGRHD KIRIIKMRRR KHYRKQQGH RQWFTELKIT GISG

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Macromolecule #18: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 11.960126 KDa
SequenceString:
MMEVTAKLRG AAISAQKARL VADLIRGKSV AHALNILNFS NKKAAVLVKK ALESAIANAE HNNSLDVDDL KVSTIYVDEG MSLKRIMPR AKGRADRITK RTCHITVKVG V

+
Macromolecule #19: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 11.607392 KDa
SequenceString:
MNNERIYQVL KGPVFSEKAQ VLGDTAGVQV FKVDINATKL EIKKAVEKLF GVEVVKVNTT ITKGKTKRFG RTLGRRSDVK KAYVTLKAG QDVEMADLGD TAESAAE

+
Macromolecule #20: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 11.187929 KDa
SequenceString:
MAKIKKGDQV IVIAGKEKGK QGTVLSVSED RVKVEGLNLV KKHQKPNRVT GAEGGIVTQE ASLHISNVAI LNATTQKADR VGYQVIDGV KTRVYKSTGE SVAVAK

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Macromolecule #21: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 10.914539 KDa
SequenceString:
MANFVLNAQA RAEDKQGKGA SRRLRRESLV PAIIYGGNAE PVAVTLELRE LVKALESNAF FEEVVEIKVG DKVENVKIQA LQRHPAKNT PMHADFKRA

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Macromolecule #22: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 9.072387 KDa
SequenceString:
MATKKAGGST KNGRDSNPKM LGVKVYGGQT VTAGNIIVRQ RGTEFHAGAN VGMGRDHTLF ATADGVVKFE VKGQFGRRYV KVETV

+
Macromolecule #23: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 9.125756 KDa
SequenceString:
MSKVCQVTGK RPVVGNNVSH ANNKTKRRFE PNLHHHRFWL ESEKRFVRLR LTTKGMRIID KLGIEKVVAD LRAQGQKI

+
Macromolecule #24: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 7.449678 KDa
SequenceString:
MKTKDLREKS VEELKALLDE QQLNQFRLRM AKATGQLGKS HEVQVARKTI ARIKTLLTEK QGNGQ

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Macromolecule #25: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 6.654788 KDa
SequenceString:
MKTIKVTQTK SSSHRLKNHK LCLQGLGLRR IGHTVEVQDT PSNRGMINKV YYMVSVEE

+
Macromolecule #26: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 7.096888 KDa
SequenceString:
MAVQQNRKSR SRRDMRRSHD ALTENALTVD QATGETHRRH HVTKDGFYRG RQLFAKAADA E

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Macromolecule #27: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 6.10531 KDa
SequenceString:
MRDKIRLVSS AGTGYFYTTT KNKRTMPEKM EIKKFDPKIR QHVIFKEAKI K

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Macromolecule #28: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 5.192247 KDa
SequenceString:
MKRTFQPSEL KRKRVHGFRA RMATKAGRQV LARRRAKGRH SLTV

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Macromolecule #29: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 7.424098 KDa
SequenceString:
MAKLKTRRGA AKRFKATANG FKRKQAFKRH ILTKKSAKRI RQLRGCVMVH VSDVASVRRM CPYI

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Macromolecule #30: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 4.276201 KDa
SequenceString:
MKVQASVKKI CGSCKVIRRN GVIRVICSAE PRHKQRQG

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Macromolecule #31: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 31 / Number of copies: 160 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: INSILICO MODEL
In silico model: Made by stochastic gradient descent in RELION 3.0
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' reconstruction. The mask used for this procedure is deposited with this entry.
Number images used: 51958
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5mdz


5afi

chain_id: w
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-6yhs:
Acinetobacter baumannii ribosome-amikacin complex - 50S subunit

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