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- EMDB-10283: Pseudomonas aeruginosa 30s ribosome from a clinical isolate -

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Basic information

Entry
Database: EMDB / ID: EMD-10283
TitlePseudomonas aeruginosa 30s ribosome from a clinical isolate
Map data
Sample
  • Complex: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
    • RNA: x 1 types
    • Protein or peptide: x 20 types
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytoplasm
Similarity search - Function
Type-1 KH domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. ...Type-1 KH domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / 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 S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / 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 S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain / Ribosomal protein S13 signature.
Similarity search - Domain/homology
Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS5 ...Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11
Similarity search - Component
Biological speciesPseudomonas aeruginos (bacteria) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHalfon Y / Jimenez-Fernande A / La Ros R / Espinos R / Krogh Johansen H / Matzov D / Eyal Z / Bashan A / Zimmerman E / Belousoff M ...Halfon Y / Jimenez-Fernande A / La Ros R / Espinos R / Krogh Johansen H / Matzov D / Eyal Z / Bashan A / Zimmerman E / Belousoff M / Molin S / Yonath A
Funding support Denmark, 4 items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4181-00115 Denmark
European Research Council322581
Novo Nordisk Foundation Denmark
European UnioniNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structure of ribosomes from an aminoglycoside-resistant clinical isolate.
Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / ...Authors: Yehuda Halfon / Alicia Jimenez-Fernandez / Ruggero La Rosa / Rocio Espinosa Portero / Helle Krogh Johansen / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Matthew Belousoff / Søren Molin / Ada Yonath /
Abstract: Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a ...Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.
History
DepositionSep 1, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6spe
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10283.png

Downloads & links

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Map

FileDownload / File: emd_10283.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.120291285 - 0.35139373
Average (Standard dev.)0.00069754454 (±0.008020044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1200.3510.001

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Supplemental data

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Sample components

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Entire : Pseudomonas aeruginosa 70s ribosome from a clinical isolate

EntireName: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
Components
  • Complex: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
    • 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

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Supramolecule #1: Pseudomonas aeruginosa 70s ribosome from a clinical isolate

SupramoleculeName: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginos (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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 494.643906 KDa
SequenceString: AACUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAGCGGAU AAAGGGAGCU UGCUCCUGG AUUCAGCGGC GGACGGGUGA GUAAUGCCUA GGAAUCUGCC UGGUAGUGGG GGAUAACGUC CGGAAACGGG C GCUAAUAC ...String:
AACUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAGCGGAU AAAGGGAGCU UGCUCCUGG AUUCAGCGGC GGACGGGUGA GUAAUGCCUA GGAAUCUGCC UGGUAGUGGG GGAUAACGUC CGGAAACGGG C GCUAAUAC CGCAUACGUC CUGAGGGAGA AAGUGGGGGA UCUUCGGACC UCACGCUAUC AGAUGAGCCU AGGUCGGAUU AG CUAGUUG GUGGGGUAAA GGCCUACCAA GGCGACGAUC CGUAACUGGU CUGAGAGGAU GAUCAGUCAC ACUGGAACUG AGA CACGGU CCAGACUCCU ACGGGAGGCA GCAGUGGGGA AUAUUGGACA AUGGGCGAAA GCCUGAUCCA GCCAUGCCGC GUGU GUGAA GAAGGUCUUC GGAUUGUAAA GCACUUUAAG UUGGGAGGAA GGGCAGUAAG UUAAUACCUU GCUGUUUUGA CGUUA CCAA CAGAAUAAGC ACCGGCUAAC UUCGUGCCAG CAGCCGCGGU AAUACGAAGG GUGCAAGCGU UAAUCGGAAU UACUGG GCG UAAAGCGCGC GUAGGUGGUU CAGCAAGUUG GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCCAA AACUACU GA GCUAGAGUAC GGUAGAGGGU GGUGGAAUUU CCUGUGUAGC GGUGAAAUGC GUAGAUAUAG GAAGGAACAC CAGUGGCG A AGGCGACCAC CUGGACUGAU ACUGACACUG AGGUGCGAAA GCGUGGGGAG CAAACAGGAU UAGAUACCCU GGUAGUCCA CGCCGUAAAC GAUGUCGACU AGCCGUUGGG AUCCUUGAGA UCUUAGUGGC GCAGCUAACG CGAUAAGUCG ACCGCCUGGG GAGUACGGC CGCAAGGUUA AAACUCAAAU GAAUUGACGG GGGCCCGCAC AAGCGGUGGA GCAUGUGGUU UAAUUCGAAG C AACGCGAA GAACCUUACC UGGCCUUGAC AUGCUGAGAA CUUUCCAGAG AUGGAUUGGU GCCUUCGGGA ACUCAGACAC AG GUGCUGC AUGGCUGUCG UCAGCUCGUG UCGUGAGAUG UUGGGUUAAG UCCCGUAACG AGCGCAACCC UUGUCCUUAG UUA CCAGCA CCUCGGGUGG GCACUCUAAG GAGACUGCCG GUGACAAACC GGAGGAAGGU GGGGAUGACG UCAAGUCAUC AUGG CCCUU ACGGCCAGGG CUACACACGU GCUACAAUGG UCGGUACAAA GGGUUGCCAA GCCGCGAGGU GGAGCUAAUC CCAUA AAAC CGAUCGUAGU CCGGAUCGCA GUCUGCAACU CGACUGCGUG AAGUCGGAAU CGCUAGUAAU CGUGAAUCAG AAUGUC ACG GUGAAUACGU UCCCGGGCCU UGUACACACC GCCCGUCACA CCAUGGGAGU GGGUUGCUCC AGAAGUAGCU AGUCUAA CC GCAAGGGGGA CGGUUACCAC GGAGUGAUUC AUGACUGGGG UGAAGUCGUA ACAAGGUAGC CGUAGGGGAA CCUGCGGC U GGAUC

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 26.684766 KDa
SequenceString: QVNMRDMLKA GVHFGHQTRY WNPKMGKFIF GARNKIHIIN LEKTLPMFNE ALTFVERLAA GKNKILFVGT KRSAGKIVRE EAARCGMPY VDHRWLGGML TNYKTIRQSI KRLRDLETQS QDGTFDKLTK KEALMRSRDL EKLERSLGGI KDMGGLPDAL F VIDVDHER ...String:
QVNMRDMLKA GVHFGHQTRY WNPKMGKFIF GARNKIHIIN LEKTLPMFNE ALTFVERLAA GKNKILFVGT KRSAGKIVRE EAARCGMPY VDHRWLGGML TNYKTIRQSI KRLRDLETQS QDGTFDKLTK KEALMRSRDL EKLERSLGGI KDMGGLPDAL F VIDVDHER IAITEANKLG IPVIGVVDTN SSPEGVDYVI PGNDDAIRAV QLYLNSMAEA VIRGKQGAAT SADEFVEEAP A

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 23.438215 KDa
SequenceString: QKVHPNGIRL GIVKEHTSVW YADRKNYADY LFADLKVREY LQDKLKSASV SRIDIHRPAQ TARITIHTAR PGIVIGKKGE DVEKLRQDL TKQMGVPVHI NIEEIRKPEL DAMLVAQSVA QQLERRVMFR RAMKRAVQNA MRIGAKGIKI QVSGRLGGAE I ARTEWYRE ...String:
QKVHPNGIRL GIVKEHTSVW YADRKNYADY LFADLKVREY LQDKLKSASV SRIDIHRPAQ TARITIHTAR PGIVIGKKGE DVEKLRQDL TKQMGVPVHI NIEEIRKPEL DAMLVAQSVA QQLERRVMFR RAMKRAVQNA MRIGAKGIKI QVSGRLGGAE I ARTEWYRE GRVPLHTLRA DIDYATYEAH TTYGVIGVKV WIFKGEV

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 23.187473 KDa
SequenceString: ARYIGPKCKL SRREGTDLFL KSGARALDSK CKAENVPGQH GQRRGRLSDY GLQLREKQKV RRIYGVLERQ FRGYYQEASR RKGSTGENL LQLLECRLDN VVYRMGFGST RSESRQLVSH KAITVNGQTV NIPSYQVKAG DVVAVREKSK NQLRIAQALE L CGQRGRVE ...String:
ARYIGPKCKL SRREGTDLFL KSGARALDSK CKAENVPGQH GQRRGRLSDY GLQLREKQKV RRIYGVLERQ FRGYYQEASR RKGSTGENL LQLLECRLDN VVYRMGFGST RSESRQLVSH KAITVNGQTV NIPSYQVKAG DVVAVREKSK NQLRIAQALE L CGQRGRVE WVEVDLDKKA GTFKSAPARS DLSADINENL IVELYSK

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 16.432092 KDa
SequenceString:
GYIEKLVQVN RVAKTVKGGR IFAFTALTVV GDGKGRVGFG RGKAREVPAA IQKAMEAARR NMIQVDLNGT TLQYPTKSAH GASKVYMQP ASEGTGIIAG GAMRAVLEVA GVQNVLAKCY GSTNPVNVVY ATFKGLKNMQ APEAVAAKRG KSVEEIL

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.278832 KDa
SequenceString:
RHYEIVFLVH PDQSEQVGGM VERYTKAIEE DGGKIHRLED WGRRQLAYAI NNVHKAHYVL MNVECSAKAL AELEDNFRYN DAVIRNLVM RRDEAVTEQS EMLKAE

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.313199 KDa
SequenceString:
RRRVAAKREV LADPKYGSQI LAKFMNHVME SGKKAVAERI VYGALDKVKE RGKADPLETF EKALDAIAPL VEVKSRRVGG ATYQVPVEV RPSRRNALAM RWLVDFARKR GEKSMALRLA GELLDAAEGK GAAVKKREDV HRMAEANKAF SHYRF

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.059415 KDa
SequenceString:
SMQDPLADML TRIRNAQMAE KTVVSMPSSK LKAAVAKVLK DEGYIADFQI SSEVKPQLSI ELKYFEGKPV IEEVKRISRP GLRQYKSVE QLPKVRGGLG VSIVSTNKGV MTDRAARAAG VGGEVLCTVF

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.139195 KDa
SequenceString:
ATQNYGTGRR KTATARVFLR PGTGKISINN RGLDQFFGRE TARMVVRQPL ELTETVEKFD IFVTVVGGGV SGQAGAIRHG ITRALIEYD ETLRSSLRKA GYVTRDAREV ERKKVGLRKA RKRPQYS

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 10.886569 KDa
SequenceString:
IRLKAFDHRL IDQSTQEIVE TAKRTGAQVR GPIPLPTRKE RFTVLISPHV NKDARDQYEI RTHKRVLDIV QPTDKTVDAL MKLDLAAGV EVQISLG

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.086657 KDa
SequenceString:
KTVVDGIAHI HASFNNTIVT ITDRQGNALS WATSGGSGFR GSRKSTPFAA QVAAERAGQA ALEYGLKNLD VNVKGPGPGR ESAVRALNA CGYKIASITD VTPIPHNGCR PPKKRR

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 13.569727 KDa
SequenceString:
ATINQLVRKP RKRMVDKSDV PALQNCPQRR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVSSYIGGEG HNLQEHSVVL IRGGRVKDL PGVRYHTVRG SLDTSGVKDR KQGRSKYGAK RP

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.307191 KDa
SequenceString:
RIAGVNIPDN KHTVISLTYI YGVGRTTAQS ICAATGVNPA AKIKDLSDEQ IDQLRNEVAK ITTEGDLRRE INMNIKRLMD LGCYRGLRH RRGLPVRGQR TKTNARTRKG P

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 11.203024 KDa
SequenceString:
KESMKNRELK RQLTVAKYAK KRAELKAIIA NPNSSAEERW NAQVALQKQP RDASASRLRN RCRLTGRPHG FYRKFGLSRN KLREAAMRG DVPGLVKAS

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 9.776193 KDa
SequenceString:
LSVEEKAQIV NEYKQAEGDT GSPEVQVALL SANINKLQDH FKANGKDHHS RRGLIRMVNQ RRKLLDYLKG KDVSRYTALI GRLGLR

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.762938 KDa
SequenceString:
MVTIRLARGG SKKRPFYHLT VTNSRNARDG RFVERIGFFN PVATGGEVRL SVDQERATYW LGQGAQPSER VAQLLKDA

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.848358 KDa
SequenceString:
RTLTGRVVSD KMDKTVTVLI ERRVKHPIYG KYVKRSTKLH AHDESNQCRI GDLVTIRETR PLAKTKAWTL VDIVER

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.346693 KDa
SequenceString:
FFRRRRFCRF TAEGVKEIDY KDLNTLKAYV SETGKIVPSR ITGTKAKYQR QLATAIKRAR YLALLPYTDS H

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 9.182882 KDa
SequenceString:
PRSLKKGPFI DLHLLKKVEV AVEKNDRKPI KTWSRRSMIL PHMVGLTIAV HNGRQHVPVL VNEDMVGHKL GEFAATRTYR

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 9.426062 KDa
SequenceString:
NTPSAKKRAK QAEKRRSHNA SLRSMVRTYI KNVVKAIDAK DLEKAQAAFT AAVPVIDRMA DKGIIHKNKA ARHKSRLSGH IKALS

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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: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 7.519769 KDa
SequenceString:
KVKENEPFDV ALRRFKRSCE KAGALAEVRS REFYEKPTAE RKRKAAAAVK RHAKKVQREQ RRR

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4lf4

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 128795

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About Yorodumi

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

New format data for meta-information of EMDB entries

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