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- EMDB-10892: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head -

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Basic information

Entry
Database: EMDB / ID: EMD-10892
TitleAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Map dataAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head, post-processed map
Sample
  • Complex: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
    • RNA: x 3 types
    • Protein or peptide: x 7 types
  • Ligand: x 1 types
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 S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / 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 S19 / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
30S ribosomal protein S7 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S14 / 30S ribosomal protein S13 / 30S ribosomal protein S9
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 21, 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: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ys5
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10892.png

Downloads & links

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Map

FileDownload / File: emd_10892.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head, post-processed map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.079076774 - 0.1765389
Average (Standard dev.)0.0000417424 (±0.0018324443)
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-0.0790.1770.000

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Supplemental data

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Mask #1

Fileemd_10892_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_10892_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 - 30S subunit head,...

Fileemd_10892_half_map_1.map
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head, 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 - 30S subunit head,...

Fileemd_10892_half_map_2.map
AnnotationAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head, 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 - 30S subunit head

EntireName: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Components
  • Complex: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
    • RNA: 16S ribosomal RNA
    • RNA: E-site tRNA
    • RNA: mRNAMessenger RNA
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14
    • Protein or peptide: 30S ribosomal protein S19
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head

SupramoleculeName: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S 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: 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

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Macromolecule #2: E-site tRNA

MacromoleculeName: E-site tRNA / type: rna / ID: 2
Details: E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs
Number of copies: 1
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 #3: mRNA

MacromoleculeName: mRNA / type: rna / ID: 3
Details: Mixture of mRNAs at the E-site, modelled as polyuridine
Number of copies: 1
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 1.179706 KDa
SequenceString:
UUUU

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Macromolecule #4: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / 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: 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

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Macromolecule #5: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 5 / Details: residues 126-145 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: 17.733699 KDa
SequenceString:
MPRRRVVAAR EILPDPKFSS QTIAKFMNHV MQDGKKSIAE SIVYGALERV QEKNKVDPVE FFETTLEKVR PMVEVKARRV GGATYQVPM EVRPSRRTAL AMRWLVDAAA KRSEKTMALR LAGELLDAAE GKGAAIKKRE DVHRMAEANK AFSHYRF

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Macromolecule #6: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 14.28761 KDa
SequenceString:
MATNYGTGRR KTATARVFLS AGTGKLVINN RTLEQYFGRE TARMVVRQPL ELLEATEKYD LYITVKGGGI GGQAGAIRHG ITRALIAAD ETLKPVLRQA GFVTRDAREV ERKKLGLRKA RKRPQFSKR

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Macromolecule #7: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Molecular weightTheoretical: 11.718531 KDa
SequenceString:
MSNQRIRIRL KSFDHRLIDQ SAQEIVETAK RTGAQVCGPI PMPTRIERFN VLTSPHVNKD ARDQYEIRTY KRLIDIVQPT DKTVDALMK LDLAAGVDVQ IALG

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Macromolecule #8: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / 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: 13.295635 KDa
SequenceString:
MARIAGVNIP DNKHAVISLT YIFGIGRHTA KNILAAVGIT ETTKIRELDD AQLDAIRAEV AKVPTEGDLR REISMNIKRL MDLGCYRGL RHRRSLPVRG QRTKTNARTR KGPRKPIKK

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Macromolecule #9: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / 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: 11.438427 KDa
SequenceString:
MAKKGMINRE LKREKTVAKY AAKRAELKAT IANVNASDEE RFEAMLKLQA LPRNASPVRL RNRCGLTGRP HGYFRKFGLS RNKLRDTVM QGDVPGVVKA SW

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Macromolecule #10: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / 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: 10.206957 KDa
SequenceString:
MPRSLKKGPF VDAHLFAKVE AAVASNSRKP IKTWSRRSMI LPDFVGLTIS VHNGRNHVPV IVTEHMVGHK LGEFAPTRTY RGHGVDKKS KR

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 24 / 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
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: 3.0 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 head' 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-6ys5:
Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head

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