[English] 日本語
Yorodumi
- EMDB-23666: A. baumannii Ribosome-Eravacycline complex: 30S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23666
TitleA. baumannii Ribosome-Eravacycline complex: 30S
Map dataCombined map of 30S-Era complex
Sample
  • Complex: A baumannii 30S ribosome in complex with Eravacycline
    • RNA: x 1 types
    • Protein or peptide: x 20 types
  • Ligand: x 3 types
KeywordsAcinetobacter baumannii / ribosome / eravacycline / antibiotic
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein 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 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / 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 S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S14 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S2, conserved site / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13-like, H2TH / Ribosomal protein S17 signature. / S4 RNA-binding domain / Ribosomal protein S5, C-terminal domain / RNA-binding S4 domain
Similarity search - Domain/homology
30S ribosomal protein S10 / 30S ribosomal protein S18 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 ...30S ribosomal protein S10 / 30S ribosomal protein S18 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2
Similarity search - Component
Biological speciesAcinetobacter baumannii AB0057 (bacteria) / Acinetobacter baumannii (strain AB0057) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsMorgan CE / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2021
Title: Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
Authors: Zhemin Zhang / Christopher E Morgan / Robert A Bonomo / Edward W Yu /
Abstract: Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections ...Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections has been to target the bacterial ribosome. However, in many cases, multidrug efflux pumps within the bacterium recognize and extrude these clinically important antibiotics designed to inhibit the protein synthesis function of the bacterial ribosome. Thus, multidrug efflux within A. baumannii and other highly drug-resistant strains is a major cause of failure of drug-based treatments of infectious diseases. We here report the first structures of the cinetobacter rug fflux (Ade)J pump in the presence of the antibiotic eravacycline, using single-particle cryo-electron microscopy (cryo-EM). We also describe cryo-EM structures of the eravacycline-bound forms of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. Our data indicate that the AdeJ pump primarily uses hydrophobic interactions to bind eravacycline, while the 70S ribosome utilizes electrostatic interactions to bind this drug. Our work here highlights how an antibiotic can bind multiple bacterial targets through different mechanisms and potentially enables drug optimization by taking advantage of these different modes of ligand binding. Acinetobacter baumannii has developed into a highly antibiotic-resistant Gram-negative pathogen. The prevalent AdeJ multidrug efflux pump mediates resistance to different classes of antibiotics known to inhibit the function of the 70S ribosome. Here, we report the first structures of the A. baumannii AdeJ pump, both in the absence and presence of eravacycline. We also describe structures of the A. baumannii ribosome bound by this antibiotic. Our results indicate that AdeJ and the ribosome use very distinct binding modes for drug recognition. Our work will ultimately enable structure-based drug discovery to combat antibiotic-resistant A. baumannii infection.
History
DepositionMar 22, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7m4u
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23666.png

Downloads & links

-
Map

FileDownload / File: emd_23666.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined map of 30S-Era complex
Voxel sizeX=Y=Z: 0.848 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.0363802 - 4.987192
Average (Standard dev.)0.0039219116 (±0.053436916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 434.176 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8480.8480.848
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z434.176434.176434.176
α/β/γ90.00090.00090.000
start NX/NY/NZ112106106
NX/NY/NZ133131160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.0364.9870.004

-
Supplemental data

-
Additional map: Focus-refined and density-modified map of 30S core from...

Fileemd_23666_additional_1.map
AnnotationFocus-refined and density-modified map of 30S core from the 30S-Era complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focus-refined and density-modified map of 30S head from...

Fileemd_23666_additional_2.map
AnnotationFocus-refined and density-modified map of 30S head from the 30S-Era complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : A baumannii 30S ribosome in complex with Eravacycline

EntireName: A baumannii 30S ribosome in complex with Eravacycline
Components
  • Complex: A baumannii 30S ribosome in complex with Eravacycline
    • RNA: 16s Ribosomal RNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S3
    • 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 S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14
    • 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 S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S21
  • Ligand: Eravacycline
  • Ligand: MAGNESIUM ION
  • Ligand: water

+
Supramolecule #1: A baumannii 30S ribosome in complex with Eravacycline

SupramoleculeName: A baumannii 30S ribosome in complex with Eravacycline / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)

+
Macromolecule #1: 16s Ribosomal RNA

MacromoleculeName: 16s Ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 500.297531 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 GAGGCUACUC UAGUUAAUAC CUAGGGAUAG UGGAC GUUA CUCGCAGAAU AAGCACCGGC UAACUCUG(PSU)G CCAGCAGCC(7MG) CGGUAAUACA GAGGGUGCGA GCGUUAAU C GGAUUUACUG GGCGUAAAGC GUGCGUAGGC GGCUUAUUAA GUCGGAUGUG AAAUCCCCGA GCUUAACUUG GGAAUUGCA UUCGAUACUG GUGAGCUAGA GUAUGGGAGA GGAUGGUAGA AUUCCAGGUG UAGCGGUGAA AUGCGUAGAG AUCUGGAGGA AUACCGAUG GCGAAGGCAG CCAUCUGGCC UAAUACUGAC GCUGAGGUAC GAAAGCAUGG GGAGCAAACA GGAUUAGAUA C CCUGGUAG UCCAUGCCGU AAACGAUGUC UACUAGCCGU UGGGGCCUUU GAGGCUUUAG UGGCGCAGCU AACGCGAUAA GU AGACCGC CUGGGGAGUA CGGUCGCAAG ACUAAAACUC AAAUGAAUUG ACGGGGGCCC GCACAAGCGG UGGAGCAUGU GGU UUAAUU CGAU(2MG)(5MC)AACG CGAAGAACCU UACCUGGCCU UGACAUACUA GAAACUUUUC AGAGAUGGAU UGGUGC CUU CGGGAACCUA GAUACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUCGUGA GAUGUUGGGU UAAGUCCCGC AACGAGC GC AACCCUUUUC CUUACUUGCC AGCAUUUCGG AUGGGAACUU UAAGGAUACU GCCAGUGACA AACUGGAGGA AGGCGGGG A CGACGUCAAG UCAUCAUG(2MG)C CCUUACGGCC AGGGCUACAC ACGUGCUACA AUGGUCGGUA CAAAGGGUUG CUACA CAGC GAUGUGAUGC UAAUCUCAAA AAGCCGAUCG UAGUCCGGAU UGGAGUCUGC AACUCGACUC CAUGAAGUCG GAAUCG CUA GUAAUCGCGG AUCAGAAUGC CGCGGUGAAU ACGUUCCCGG GCCUUGUACA CACCG(4OC)CCGU CACACCAUGG GAG UUUGUU GCACCAGAAG UAGCUAGCCU AACUGCAAAG AGGGCGGUUA CCACGGUGUG GCCGAUGACU GGGGUGAAGU CG (UR3)AACAAG GUAGCCGUAG GGG(MA6)(MA6)CCUGC GGCUGGAUCA CCUCCUUAAC GAA

GENBANK: GENBANK: CP001182.2

+
Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 27.972461 KDa
SequenceString: MGQKVHPIGI RLGVVKRHNA NWYANPKQYA EYLLKDLQVR EFLTKKLKNA MVSNILIERP SGAAKVTIST ARPGIVIGKK GEDIEKLQR ELTNIMGVPA QVSINEIDRP DLDARLVAEA IASQLEKRVM FRRAMKRAVQ NTMRAGAKGI KVEVSGRLGG A EIARTEWY ...String:
MGQKVHPIGI RLGVVKRHNA NWYANPKQYA EYLLKDLQVR EFLTKKLKNA MVSNILIERP SGAAKVTIST ARPGIVIGKK GEDIEKLQR ELTNIMGVPA QVSINEIDRP DLDARLVAEA IASQLEKRVM FRRAMKRAVQ NTMRAGAKGI KVEVSGRLGG A EIARTEWY REGRVPLHTL RADIDYATMR AETTYGTIGV KVWIFRGEIL GGMKQVMNPA PAEERPAKRG RGRGEGQERR GR RGDRAAD KGE

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 17.733699 KDa
SequenceString:
MPRRRVVAAR EILPDPKFSS QTIAKFMNHV MQDGKKSIAE SIVYGALERV QEKNKVDPVE FFETTLEKVR PMVEVKARRV GGATYQVPM EVRPSRRTAL AMRWLVDAAA KRSEKTMALR LAGELLDAAE GKGAAIKKRE DVHRMAEANK AFSHYRF

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 14.28761 KDa
SequenceString:
MATNYGTGRR KTATARVFLS AGTGKLVINN RTLEQYFGRE TARMVVRQPL ELLEATEKYD LYITVKGGGI GGQAGAIRHG ITRALIAAD ETLKPVLRQA GFVTRDAREV ERKKLGLRKA RKRPQFSKR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 11.718531 KDa
SequenceString:
MSNQRIRIRL KSFDHRLIDQ SAQEIVETAK RTGAQVCGPI PMPTRIERFN VLTSPHVNKD ARDQYEIRTY KRLIDIVQPT DKTVDALMK LDLAAGVDVQ IALG

UniProtKB: 30S ribosomal protein S10

+
Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (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

+
Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 13.295635 KDa
SequenceString:
MARIAGVNIP DNKHAVISLT YIFGIGRHTA KNILAAVGIT ETTKIRELDD AQLDAIRAEV AKVPTEGDLR REISMNIKRL MDLGCYRGL RHRRSLPVRG QRTKTNARTR KGPRKPIKK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #14: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 11.438427 KDa
SequenceString:
MAKKGMINRE LKREKTVAKY AAKRAELKAT IANVNASDEE RFEAMLKLQA LPRNASPVRL RNRCGLTGRP HGYFRKFGLS RNKLRDTVM QGDVPGVVKA SW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #15: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 10.1456 KDa
SequenceString:
MALTNADRAE IIAKFARAEN DTGSPEVQVA LLTAQINDLQ GHFKAHKHDH HSRRGLIRMV NQRRKLLDYL NGKDHERYTA LIGALGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #16: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 11.22306 KDa
SequenceString:
MLPMVGAGII RKNYKAFIMV VIRLARGGAK KRPFYQIVVT DSRNARDGRF IERIGFFNPT AQGQAEKLRL DADRFAHWVS QGAQPSERV ASLAAQAKKA TA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #17: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 9.543101 KDa
SequenceString:
MSEKTVRTLT GKVVSDKMDK SIVVLIERRV QHPLYGKSIR RSTKLHAHDE NNVAKIGDVV TIKESRPISK TKAWTLVEVV EAAAE

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #18: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 9.009452 KDa
SequenceString:
MARFYRRRKF CRFTAENVAY IDYKDIDTLK QYITENGKIV PSRITGTKAR YQRQLALAIK QARYLSLIPY TDNHK

UniProtKB: 30S ribosomal protein S18

+
Macromolecule #19: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 10.206957 KDa
SequenceString:
MPRSLKKGPF VDAHLFAKVE AAVASNSRKP IKTWSRRSMI LPDFVGLTIS VHNGRNHVPV IVTEHMVGHK LGEFAPTRTY RGHGVDKKS KR

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #20: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 9.72342 KDa
SequenceString:
MANSAQAKKR ARQNVKARKH NASLRSMVRT YIKRTLSAIA GGDYAVATEA YKKAVPVIDR MADKGIIHKN KAARHKSRLN AQVKALAN

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #21: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Molecular weightTheoretical: 8.474033 KDa
SequenceString:
MPQVKLKEGE PVDVAIRRFK RSCEKAGVLA DVRKREFYEK PTQERKRKKA AAVKRYQKKL ARESVRTTRL Y

UniProtKB: Small ribosomal subunit protein bS21

+
Macromolecule #22: Eravacycline

MacromoleculeName: Eravacycline / type: ligand / ID: 22 / Number of copies: 1 / Formula: YQM
Molecular weightTheoretical: 558.555 Da
Chemical component information

ChemComp-YQM:
Eravacycline / antibiotic*YM / Eravacycline

+
Macromolecule #23: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 83 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 191 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Resolution of 30S core = 2.80. Resolution of 30S head = 2.71.
Number images used: 47367

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more