[English] 日本語
Yorodumi
- EMDB-10282: Pseudomonas aeruginosa 50s ribosome from a clinical isolate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10282
TitlePseudomonas aeruginosa 50s ribosome from a clinical isolate
Map data
Sample
  • Complex: Pseudomonas aeruginosa 70s ribosome from a clinical isolate
    • RNA: x 2 types
    • Protein or peptide: x 30 types
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24
Similarity search - Domain/homology
Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 ...Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36
Similarity search - Component
Biological speciesPseudomonas aeruginos (bacteria) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0566
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0566
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6spd
  • Surface level: 0.0566
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10282.png

Downloads & links

-
Map

FileDownload / File: emd_10282.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: 0.0566 / Movie #1: 0.0566
Minimum - Maximum-0.2330923 - 0.5138056
Average (Standard dev.)0.001234065 (±0.013298968)
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-0.2330.5140.001

-
Supplemental data

-
Additional map: Unsharp map

Fileemd_10282_additional.map
AnnotationUnsharp map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L11
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: Ribosomal protein uL29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36

+
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)

+
Macromolecule #1: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 935.951375 KDa
SequenceString: GUCAAGUGAA GAAGCGCAUA CGGUGGAUGC CUUGGCAGUC AGAGGCGAUG AAAGACGUGG UAGCCUGCGA AAAGCUUCGG GGAGUCGGC AAACAGACUU UGAUCCGGAG AUCUCUGAAU GGGGGAACCC ACCUAGGAUA ACCUAGGUAU CUUGUACUGA A UCCAUAGG ...String:
GUCAAGUGAA GAAGCGCAUA CGGUGGAUGC CUUGGCAGUC AGAGGCGAUG AAAGACGUGG UAGCCUGCGA AAAGCUUCGG GGAGUCGGC AAACAGACUU UGAUCCGGAG AUCUCUGAAU GGGGGAACCC ACCUAGGAUA ACCUAGGUAU CUUGUACUGA A UCCAUAGG UGCAAGAGGC GAACCAGGGG AACUGAAACA UCUAAGUACC CUGAGGAAAA GAAAUCAACC GAGAUUCCCU UA GUAGUGG CGAGCGAACG GGGAUUAGCC CUUAAGCUUC AUUGAUUUUA GCGGAACGCU CUGGAAAGUG CGGCCAUAGU GGG UGAUAG CCCCGUACGC GAAAGGAUCU UUGAAGUGAA AUCAAGUAGG ACGGAGCACG AGAAACUUUG UCUGAACAUG GGGG GACCA UCCUCCAAGG CUAAAUACUA CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAAGAACC CCGGA GAGG GGAGUGAAAU AGAACCUGAA ACCGUAUGCG UACAAGCAGU GGGAGCCUAC UUGUUAGGUG ACUGCGUACC UUUUGU AUA AUGGGUCAGC GACUUAUAUU CAGUGGCAAG CUUAACCGUA UAGGGUAGGC GUAGCGAAAG CGAGUCUUAA UAGGGCG UU UAGUCGCUGG GUAUAGACCC GAAACCGGGC GAUCUAUCCA UGAGCAGGUU GAAGGUUAGG UAACACUGAC UGGAGGAC C GAACCCACUC CCGUUGAAAA GGUAGGGGAU GACUUGUGGA UCGGAGUGAA AGGCUAAUCA AGCUCGGAGA UAGCUGGUU CUCCUCGAAA GCUAUUUAGG UAGCGCCUCA UGUAUCACUC UGGGGGGUAG AGCACUGUUU CGGCUAGGGG GUCAUCCCGA CUUACCAAA CCGAUGCAAA CUCCGAAUAC CCAGAAGUGC CGAGCAUGGG AGACACACGG CGGGUGCUAA CGUCCGUCGU G AAAAGGGA AACAACCCAG ACCGCCAGCU AAGGUCCCAA AGUUGUGGUU AAGUGGUAAA CGAUGUGGGA AGGCUUAGAC AG CUAGGAG GUUGGCUUAG AAGCAGCCAC CCUUUAAAGA AAGCGUAAUA GCUCACUAGU CGAGUCGGCC UGCGCGGAAG AUG UAACGG GGCUCAAACC ACACACCGAA GCUGCGGGUG UCACGUAAGU GACGCGGUAG AGGAGCGUUC UGUAAGCCUG UGAA GGUGA GUUGAGAAGC UUGCUGGAGG UAUCAGAAGU GCGAAUGCUG ACAUGAGUAA CGACAAUGGG UGUGAAAAAC ACCCA CGCC GAAAGACCAA GGGUUCCUGC GCAACGUUAA UCGACGCAGG GUUAGUCGGU UCCUAAGGCG AGGCUGAAAA GCGUAG UCG AUGGGAAACA GGUUAAUAUU CCUGUACUUC UGGUUACUGC GAUGGAGGGA CGGAGAAGGC UAGGCCAGCU UGGCGUU GG UUGUCCAAGU UUAAGGUGGU AGGCUGAAAU CUUAGGUAAA UCCGGGGUUU CAAGGCCGAG AGCUGAUGAC GAGUCGUC U UUUAGAUGAC GAAGUGGUUG AUGCCAUGCU UCCAAGAAAA GCUUCUAAGC UUCAGGUAAC CAGGAACCGU ACCCCAAAC CGACACAGGU GGUCGGGUAG AGAAUACCAA GGCGCUUGAG AGAACUCGGG UGAAGGAACU AGGCAAAAUG GCACCGUAAC UUCGGGAGA AGGUGCGCCG GCUAGGGUGA AGGAUUUACU CCGUAAGCUC UGGCUGGUCG AAGAUACCAG GCCGCUGCGA C UGUUUAUU AAAAACACAG CACUCUGCAA ACACGAAAGU GGACGUAUAG GGUGUGACGC CUGCCCGGUG CCGGAAGGUU AA UUGAUGG GGUUAGCGCA AGCGAAGCUC UUGAUCGAAG CCCCGGUAAA CGGCGGCCGU AACUAUAACG GUCCUAAGGU AGC GAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAACG AUGGCGGCGC UGUCUCCACC CGAGACUCAG UGAA AUUGA AAUCGCUGUG AAGAUGCAGU GUAUCCGCGG CUAGACGGAA AGACCCCGUG AACCUUUACU GUAGCUUUGC ACUGG ACUU UGAGCCUGCU UGUGUAGGAU AGGUGGGAGG CUUUGAAGCG UGGACGCCAG UUCGCGUGGA GCCAUCCUUG AAAUAC CAC CCUGGCAUGC UUGAGGUUCU AACUCUGGUC CGUAAUCCGG AUCGAGGACA GUGUAUGGUG GGCAGUUUGA CUGGGGC GG UCUCCUCCUA AAGAGUAACG GAGGAGUACG AAGGUGCGCU CAGACCGGUC GGAAAUCGGU CGCAGAGUAU AAAGGCAA A AGCGCGCUUG ACUGCGAGAC AGACACGUCG AGCAGGUACG AAAGUAGGUC UUAGUGAUCC GGUGGUUCUG UAUGGAAGG GCCAUCGCUC AACGGAUAAA AGGUACUCCG GGGAUAACAG GCUGAUACCG CCCAAGAGUU CAUAUCGACG GCGGUGUUUG GCACCUCGA UGUCGGCUCA UCACAUCCUG GGGCUGAAGC CGGUCCCAAG GGUAUGGCUG UUCGCCAUUU AAAGUGGUAC G CGAGCUGG GUUUAGAACG UCGUGAGACA GUUCGGUCCC UAUCUGCCGU GGACGUUUGA GAUUUGAGAG GGGCUGCUCC UA GUACGAG AGGACCGGAG UGGACGAACC UCUGGUGUUC CGGUUGUCAC GCCAGUGGCA UUGCCGGGUA GCUAUGUUCG GAA AAGAUA ACCGCUGAAA GCAUCUAAGC GGGAAACUUG CCUCAAGAUG AGAUCUCACU GGGAACUUGA UUCCCCUGAA GGGC CGUCG AAGACUACGA CGUUGAUAGG CUGGGUGUGU AAGCGUUGUG AGGCGUUGAG CUAACCAGUA CUAAUUGCCC GUGAG GCUU GACC

+
Macromolecule #2: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.335164 KDa
SequenceString:
UUGACGAUCA UAGAGCGUUG GAACCACCUG AUCCCUUCCC GAACUCAGAA GUGAAACGAC GCAUCGCCGA UGGUAGUGUG GGGUCUCCC CAUGUGAGAG UAGGUCAUCG UCAAGCU

+
Macromolecule #3: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 29.438982 KDa
SequenceString: IVKCKPTSAG RRFVVKVVNQ ELHKGAPYAP LLEKKSKSGG RNNNGRITTR HIGGGHKQHY RLVDFRRNKD GIPAIVERVE YDPNRTAHI ALLKYADGER RYIIAPKGVA AGDQLISGIG APIKAGNSMP LRNIPVGSTV HGIELKPGKG AQIARSAGAS A QLVAREGA ...String:
IVKCKPTSAG RRFVVKVVNQ ELHKGAPYAP LLEKKSKSGG RNNNGRITTR HIGGGHKQHY RLVDFRRNKD GIPAIVERVE YDPNRTAHI ALLKYADGER RYIIAPKGVA AGDQLISGIG APIKAGNSMP LRNIPVGSTV HGIELKPGKG AQIARSAGAS A QLVAREGA YVTLRLRSGE MRKVLAECRA TLGEVSNSEH SLRSLGKAGA TRWRGVRPTV RGVAMNPVDH PHGGGEGRTS AG RHPVSPW GLQTKGKKTR SNKRTDNMIV RRRK

+
Macromolecule #4: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 22.17915 KDa
SequenceString: IGVVGRKCGM TRIFTEEGVS IPVTVIEVEP NRVTQFKTEE TDGYRAVQVT AGERRASRVT KAQAGHFAKA NVAAGRGVWE FRLGEEQYA AGDQITVDLF QAGQMVDVTG ESKGKGFAGT IKRWNFRGQD NTHGNSVSHR VPGSIGQCQT PGRVFKGKKM S GHLGAERV ...String:
IGVVGRKCGM TRIFTEEGVS IPVTVIEVEP NRVTQFKTEE TDGYRAVQVT AGERRASRVT KAQAGHFAKA NVAAGRGVWE FRLGEEQYA AGDQITVDLF QAGQMVDVTG ESKGKGFAGT IKRWNFRGQD NTHGNSVSHR VPGSIGQCQT PGRVFKGKKM S GHLGAERV TVQSLEIVRV DAERNLLLVK GAVPGATGGD VIVRPAAKA

+
Macromolecule #5: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.542744 KDa
SequenceString: QLNVNGAQAI EVSERTFGGE FNETLVHQAV VAYMAGGRQG SKAQKTRSEV SGGGKKPWRQ KGTGRARAGT IRSPIWRGGG TTFAAKPRS HEQKLNKKMY RAALRSILAE LVRLDRLVVV ADFAVDAPKT KGLVAKLDTL GLKDVLIVTD GVDENLYLAA R NLAHVDVR ...String:
QLNVNGAQAI EVSERTFGGE FNETLVHQAV VAYMAGGRQG SKAQKTRSEV SGGGKKPWRQ KGTGRARAGT IRSPIWRGGG TTFAAKPRS HEQKLNKKMY RAALRSILAE LVRLDRLVVV ADFAVDAPKT KGLVAKLDTL GLKDVLIVTD GVDENLYLAA R NLAHVDVR DVQGSDPVSL IAYDKVLVTV SAVKKFEELL G

+
Macromolecule #6: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.95126 KDa
SequenceString:
RLKELYRKEI APKLKEELQL ANVMEVPRVT KITLNMGLGE AVGDKKIIEN AVADLEKITG QKPVVTYARK SIAGFKIREG WPIGVKVTL RSDRMYEFLD RLLSISLPRV RDFRGLNAKS FDGRGNYSMG VKEQIIFPEI DYDKIDALRG LDITLTTTAR T DDEGRALL RAFKFPF

+
Macromolecule #7: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 18.610406 KDa
SequenceString:
SRVAKNPVKL PAGVEIKLAG QQLSIKGAKG ALELKVHPSV EVIQDSGELR FAARNGDQQT RAMAGTTRAL VNNMVVGVSQ GFERKLQLV GVGYKAQAKG QVLSLSLGFS HPVDYELPAG IVAETPSQTD ILIKGIDKQL VGQVAAEIRD FRPPEPYKGK G VRYADEVV RRKEA

+
Macromolecule #8: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.420484 KDa
SequenceString:
EVILLEKVAN LGNLGDKVNI KGGYARNFLL PQGKATVATA ENVAAFEARR AELEKAAAEK KAAAEARAAQ LSELVVTLGA HAGDEGKLF GSIGTRDIAE AVSAAGYPLE KAEVRLPNGA LRNTGEFDVA VHLHTDVETT LKLIIVAE

+
Macromolecule #9: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.623716 KDa
SequenceString:
KKIQAYIKLQ VKAGQANPSP PVGPALGQHG VNIMEFCKAF NAKTQGQEPG LPTPVIITVY SDRSFTFETK STPAAVLLKK AAGITSGSA RPNSQKVGTV TRAQLEEIAK TKQADLTAAD LDAAVRTIAG SARSMGLNVE G

+
Macromolecule #10: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.927382 KDa
SequenceString:
KTYTAKPETV QRDWFVVDAA GQTLGRLATE IARRLRGKHK PEYTPHVDTG DYIVVINAEQ VRVTGAKTTD KMYYHHSGFP GGIKSINFE KLIAKAPERV IETAVKGMLP KNPLGRDMYR KLKVYKGASH PHTAQQPQEL KI

+
Macromolecule #11: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 13.223621 KDa
SequenceString:
MIQTQSMLDV ADNSGARRVM CIKVLGGSHR RYAGIGDIIK VTVKEAIPRG KVKKGQVMTA VVVRTKHGVR RTDGSIIRFD GNAAVLLNN KQEPIGTRIF GPVTRELRTE KFMKIVSLAP E

+
Macromolecule #12: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.073291 KDa
SequenceString:
QLNDLRSAPG ARREKHRPGR GIGSGLGKTG GRGHKGLTSR SGGKVAPGFE GGQQPLHRRL PKFGFVSLKA MDRAEVRTSE LAKVEGDVV SLQTLKDANL INQHVQRVKV MLSGEVGRAV TLKGIAATKG ARAAIEAAGG KFED

+
Macromolecule #13: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.203902 KDa
SequenceString:
MLQPKRTKFR KQMTGHNRGL AHRGSKVSFG EYALKATSRG RLTARQIESA RRALTRHVKR GGKIWIRVFP DKPVTKKPLE VRMGKGKGG VEYWVAQIQP GKVLYEIEGV SEELAREAFA LAAAKLPLAT SFVKRT

+
Macromolecule #14: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 13.495789 KDa
SequenceString:
MRHRKSGRHL SRTSAHRKAM FQNMAVSLFE HELIKTTLPK AKELRRVAEP LITLAKEDSV ANRRLAFDRT RSKAAVGKLF NDLGKRYAN RPGGYLRILK CGFRAGDNAP MAYVELVDR

+
Macromolecule #15: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.55647 KDa
SequenceString:
SVKKETRLRR ARKARLKMRE LETVRLCVYR SSQHIYAQVI AADGGKVLAS ASTLDKDLRE GATGNIDAAK KVGQLVAERA KAAGVTQVA FDRSGFKYHG RVKALADAAR EGGLEF

+
Macromolecule #16: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.708824 KDa
SequenceString:
KIIQQIEAEQ MNKEIPAFAP GDTVIVQVKV KEGDRQRLQA FEGVVIAKRN RGLNSAFTVR KISNGVGVER TFQTYSPIVD SLSVKRRGD VRKAKLYYLR ALSGKAARIK EKLV

+
Macromolecule #17: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 13.266776 KDa
SequenceString:
ARVKRGVIAR RRHKKILKLA KGYYGARSRV FRVAKQAVIK AGQYAYRDRR QRKRQFRALW IARINAGARQ NGLSYSRLIA GLKKAAIEI DRKVLADLAV NEKAAFTAIV EKAKASLA

+
Macromolecule #18: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 11.678621 KDa
SequenceString:
MYAVIVTGGK QHKVTEGEFL KVEKLDVATG EAIDFDRVLL VANGEDVKIG LPVVEGAKVT AEVVSHGRHD KVRIIKFRRR KHHMKRQGH RQWFTEIKIT GIQA

+
Macromolecule #19: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 11.804801 KDa
SequenceString:
EVAAKLSGAR ISAQKARLVA DQIRGKKVGE ALNLLAFSSK KAAEIMKKVL ESAVANAEHN EGADVDDLKV STVFVNEGRS LKRIMPRAK GRADRIVKRS CHITVKVADK

+
Macromolecule #20: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 10.231894 KDa
SequenceString:
NQERVFKVLL GPHISEKATG LADGKSQFVF KVATDATKLE IKKAVESLFS VKVQRVTTLN VKGKTKRTAR GLGKRNDWKK AYIALQPGQ DLD

+
Macromolecule #21: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 11.423413 KDa
SequenceString:
MQKIRRDDEV IVIAGKDKGK RGKVLKVLAD DRLVVGGVNL IKRHTKPNPM LGQQGGIVEK EAPLHVSNVA IFNTETSKAD RVGFKVEDG KKIRVFKSTQ KPVQ

+
Macromolecule #22: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 20.346504 KDa
SequenceString:
FIVNAQVRSD LGKGASRRLR RNAGLVPAVV YGGDKEPQSV TLELREIAKL LENEAAFSHV IALNVGGVKE TVLIKALQRH PAKGFVMHA DFLRVVADHK LTAHVPLHFI NEEVAVGVKQ AGGEISHTIS EVEVSCLPKD LPEFIEVDMA KVELGQIVHL S DLKAPKGV ELVQLAHGND LAVANIHASR

+
Macromolecule #23: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.124437 KDa
SequenceString:
TRNGRDSESK RLGVKLFGGQ AVKAGNILVR LRGTKFHAGY GVGLGKDHTL FAKVDGVVKF ETKGAFGRKY VSIVAA

+
Macromolecule #24: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.956437 KDa
SequenceString:
SRVCQVTGKG PVTGNNISHA HNKTRRRFLP NLQHHRFWVE SEKRFVRLRV SAKGMRIIDK RGIEAVLADL RARGEKF

+
Macromolecule #25: Ribosomal protein uL29

MacromoleculeName: Ribosomal protein uL29 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 6.807757 KDa
SequenceString:
KANELREEKS GPVTGNNISH LLRDQFNLRM QKATGQLGQS HLLSQVKRDI ARVKTVLNQQ

+
Macromolecule #26: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 6.358448 KDa
SequenceString:
ATVKVTLVKS LNGRLANHKA CVKGLGLRRI NHTVEVQDTP ENRGMINKAY YLLRVEG

+
Macromolecule #27: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 3.368921 KDa
SequenceString:
KADIHPTYEA IEATCSCGNV IKTRSTLCKP I

+
Macromolecule #28: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 6.043777 KDa
SequenceString:
AVQQNKKSRS ARDMRRSHDA LESNALSVEK STGEVHLRHH VSPDGFYRGR KVV

+
Macromolecule #29: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 5.928945 KDa
SequenceString:
RELIRLVSSA GTGHFYTTDK NKRTKPEKIE IKKYDPVVRQ HVIYKEAKIK

+
Macromolecule #30: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 5.226309 KDa
SequenceString:
MKRTFQPSTL KRARVHGFRA RMATKNGRQV LSRRRAKGRK RLTV

+
Macromolecule #31: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 7.2568 KDa
SequenceString:
PKMKTKSGAA KRFKKTAGGL KHKHAFKSHI LTKMTTKRKR QLRGTSMLNK SDVARVERSL RLR

+
Macromolecule #32: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 4.447445 KDa
SequenceString:
MKVRASVKKL CRNCKIIRRD GIVRVICSAE PRHKQRQG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

-
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: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 128795

+
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