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- EMDB-10914: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni... -

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Basic information

Entry
Database: EMDB / ID: EMD-10914
TitleAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
Map dataAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body, post-processed map
Sample
  • Complex: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
    • RNA: x 1 types
    • Protein or peptide: x 13 types
  • Ligand: x 1 types
Keywordsantibiotic / tigecycline / translation / ribosome
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesAcinetobacter baumannii (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
DepositionApr 24, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6yt9
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10914.png

Downloads & links

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Map

FileDownload / File: emd_10914.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body, post-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.27918893 - 0.54495555
Average (Standard dev.)0.00022779037 (±0.0075380486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.000426.000426.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2790.5450.000

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Supplemental data

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Mask #1

Fileemd_10914_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-tigecycline complex - consensus map filtered...

Fileemd_10914_additional.map
AnnotationAcinetobacter baumannii ribosome-tigecycline 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-tigecycline complex - 30S subunit body,...

Fileemd_10914_half_map_1.map
AnnotationAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body, 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-tigecycline complex - 30S subunit body,...

Fileemd_10914_half_map_2.map
AnnotationAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body, 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-tigecycline complex - 30S subuni...

EntireName: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
Components
  • Complex: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
    • RNA: 16S ribosomal RNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S21
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni...

SupramoleculeName: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 500.126156 KDa
SequenceString: UUUAACUGAA GAGUUUGAUC AUGGCUCAGA UUGAACGCUG GCGGCAGGCU UAACACAUGC AAGUCGAGCG GGGGAAGGUA GCUUGCUAC CGGACCUAGC GGCGGACGGG UGAGUAAUGC UUAGGAAUCU GCCUAUUAGU GGGGGACAAC AUCUCGAAAG G GAUGCUAA ...String:
UUUAACUGAA GAGUUUGAUC AUGGCUCAGA UUGAACGCUG GCGGCAGGCU UAACACAUGC AAGUCGAGCG GGGGAAGGUA GCUUGCUAC CGGACCUAGC GGCGGACGGG UGAGUAAUGC UUAGGAAUCU GCCUAUUAGU GGGGGACAAC AUCUCGAAAG G GAUGCUAA UACCGCAUAC GUCCUACGGG AGAAAGCAGG GGAUCUUCGG ACCUUGCGCU AAUAGAUGAG CCUAAGUCGG AU UAGCUAG UUGGUGGGGU AAAGGCCUAC CAAGGCGACG AUCUGUAGCG GGUCUGAGAG GAUGAUCCGC CACACUGGGA CUG AGACAC GGCCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGG ACAAUGGGGG GAACCCUGAU CCAGCCAUGC CGCG UGUGU GAAGAAGGCC UUAUGGUUGU AAAGCACUUU AAGCGAGGAG GAGGCUACUU UAGUUAAUAC CUAGAGAUAG UGGAC GUUA CUCGCAGAAU AAGCACCGGC UAACUCUGUG CCAGCAGCCG CGGUAAUACA GAGGGUGCGA GCGUUAAUCG GAUUUA CUG GGCGUAAAGC GUGCGUAGGC GGCUUAUUAA GUCGGAUGUG AAAUCCCCGA GCUUAACUUG GGAAUUGCAU UCGAUAC UG GUGAGCUAGA GUAUGGGAGA GGAUGGUAGA AUUCCAGGUG UAGCGGUGAA AUGCGUAGAG AUCUGGAGGA AUACCGAU G GCGAAGGCAG CCAUCUGGCC UAAUACUGAC GCUGAGGUAC GAAAGCAUGG GGAGCAAACA GGAUUAGAUA CCCUGGUAG UCCAUGCCGU AAACGAUGUC UACUAGCCGU UGGGGCCUUU GAGGCUUUAG UGGCGCAGCU AACGCGAUAA GUAGACCGCC UGGGGAGUA CGGUCGCAAG ACUAAAACUC AAAUGAAUUG ACGGGGGCCC GCACAAGCGG UGGAGCAUGU GGUUUAAUUC G AUGCAACG CGAAGAACCU UACCUGGCCU UGACAUACUA GAAACUUUCC AGAGAUGGAU UGGUGCCUUC GGGAAUCUAG AU ACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUCGUGA GAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUUUCC UUA CUUGCC AGCAUUUCGG AUGGGAACUU UAAGGAUACU GCCAGUGACA AACUGGAGGA AGGCGGGGAC GACGUCAAGU CAUC AUGGC CCUUACGGCC AGGGCUACAC ACGUGCUACA AUGGUCGGUA CAAAGGGUUG CUACACAGCG AUGUGAUGCU AAUCU CAAA AAGCCGAUCG UAGUCCGGAU UGGAGUCUGC AACUCGACUC CAUGAAGUCG GAAUCGCUAG UAAUCGCGGA UCAGAA UGC CGCGGUGAAU ACGUUCCCGG GCCUUGUACA CACCGCCCGU CACACCAUGG GAGUUUGUUG CACCAGAAGU AGCUAGC CU AACUGCAAAG AGGGCGGUUA CCACGGUGUG GCCGAUGACU GGGGUGAAGU CGUAACAAGG UAGCCGUAGG GGAACCUG C GGCUGGAUCA CCUCCUUAAC GAA

GENBANK: GENBANK: CP009534.1

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Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Details: modelled without side chains / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 27.680357 KDa
SequenceString: MADYNVSMRD LLQAGAHFGH QTRFWNPKMR QYIFGARNKI HIINLEHTVP ALNDALNFAN QLASKKNKVL FVGTKRAASN IIREQAQRA GQPYVDHRWL GGMLTNWKTL RQSINRLKDL QTQSQDGTFA KLTKREALER TREMEKLERS LGGVKNMGGL P DALFVIDV ...String:
MADYNVSMRD LLQAGAHFGH QTRFWNPKMR QYIFGARNKI HIINLEHTVP ALNDALNFAN QLASKKNKVL FVGTKRAASN IIREQAQRA GQPYVDHRWL GGMLTNWKTL RQSINRLKDL QTQSQDGTFA KLTKREALER TREMEKLERS LGGVKNMGGL P DALFVIDV DHEAIAIKEA KNLGIPVIGI VDTNSNPDNV DYVIPGNDDA IRAVTLYASA MADAILAGKE YAQSQANAQA KG DDAAKDA SEA

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #3: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 3
Details: residues 23-30 and 43-51 modelled without side chains
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 23.311818 KDa
SequenceString: MARYIGPKCK LSRREGTDLQ LKSGVKPFDV KTKKANKAPG QHGQARGGKQ SEYSLQLREK QKVRRIYGVL ERQFSNYYKE AARVKGATG ENLLKLLESR LDNVVYRMGF GSTRAEARQL VSHRSITLNG RRVNIASIQV KAGDVIAVHE GAKQQLRIKN A IELAAQRG ...String:
MARYIGPKCK LSRREGTDLQ LKSGVKPFDV KTKKANKAPG QHGQARGGKQ SEYSLQLREK QKVRRIYGVL ERQFSNYYKE AARVKGATG ENLLKLLESR LDNVVYRMGF GSTRAEARQL VSHRSITLNG RRVNIASIQV KAGDVIAVHE GAKQQLRIKN A IELAAQRG IPAWIEVDHS KLEGTFKAAP DRSDLPAEIN ESLIVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #4: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 17.181766 KDa
SequenceString:
MAKVEQNEGL VEKLVAVDRV AKVVKGGRIF SFTALTVVGD GNGRVGFGRG KAREVPAAIS KALEAARRNM ITVDLAGTTL QHPVNARHG ASRVYMQPAS EGTGVIAGGA MRAVLEAAGV HNVLAKCYGS TNAANVVNAT FKGLRDMTSP EKVAAKRGKS V EEIQG

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #5: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 14.986952 KDa
SequenceString:
MRHYEIVLLV HPDQSDQVVG MVERYISQIK EADGQIHRLE DWGRRQLAYP INKIHKAHYI LMNVECGQST LDELEELFRY NDAIIRNLI IRREHAITEE SLLAKSAEEK RARKAQREEA QQVAQEAE

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #6: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 14.250667 KDa
SequenceString:
MSMQDTVADM LTRVRNAQMA KKQTVSMPSS KLKVAIANVL QQEGYISNVE VAQEETKSTL TITLKYFEGK PVIEMVKRVS RPGLRQYRG KDKLPSVKQG LGIAIVSTSK GIMTDRAARA AGIGGEVIAF VS

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #7: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 13.558512 KDa
SequenceString:
MAKDTRTRKK VTRTVSEGVA HIHASFNNTI VTITDRQGNA LAWATSGGQG FRGSRKSTPF AAQVAAEVAG KAALDYGLKN LDVLVKGPG PGRESAVRAL GAVGYKINSI TDVTPIPHNG CRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #8: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 13.797134 KDa
SequenceString:
MATTNQLIRK GRTTLVEKSK VPALKACPQR RGVCTRVYTT TPKKPNSAMR KVCRVRLTSG FEVSSYIGGE GHNLQEHSVV LIRGGRVKD LPGVRYHTVR GSLDCAGVKD RNQSRSKYGA KRPKK

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #9: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 10.1456 KDa
SequenceString:
MALTNADRAE IIAKFARAEN DTGSPEVQVA LLTAQINDLQ GHFKAHKHDH HSRRGLIRMV NQRRKLLDYL NGKDHERYTA LIGALGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #10: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 9.215529 KDa
SequenceString:
MVVIRLARGG AKKRPFYQIV VTDSRNARDG RFIERIGFFN PTAQGQAEKL RLDADRFAHW VSQGAQPSER VASLAAQAKK ATA

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #11: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 9.543101 KDa
SequenceString:
MSEKTVRTLT GKVVSDKMDK SIVVLIERRV QHPLYGKSIR RSTKLHAHDE NNVAKIGDVV TIKESRPISK TKAWTLVEVV EAAAE

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #12: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 9.009452 KDa
SequenceString:
MARFYRRRKF CRFTAENVAY IDYKDIDTLK QYITENGKIV PSRITGTKAR YQRQLALAIK QARYLSLIPY TDNHK

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #13: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 9.72342 KDa
SequenceString:
MANSAQAKKR ARQNVKARKH NASLRSMVRT YIKRTLSAIA GGDYAVATEA YKKAVPVIDR MADKGIIHKN KAARHKSRLN AQVKALAN

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #14: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 14 / Details: residues 2-36 modelled without side chains / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 8.474033 KDa
SequenceString:
MPQVKLKEGE PVDVAIRRFK RSCEKAGVLA DVRKREFYEK PTQERKRKKA AAVKRYQKKL ARESVRTTRL Y

UniProtKB: Small ribosomal subunit protein bS21

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 56 / Formula: MG
Molecular weightTheoretical: 24.305 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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.1 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Made by stochastic gradient descent in RELION 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 '30S subunit body' reconstruction. The mask used for this procedure is deposited with this entry.
Number images used: 231159
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5mdz

source_name: PDB, initial_model_type: experimental model

5afi

chain_id: w, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-6yt9:
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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