6SPG

Pseudomonas aeruginosa 70s ribosome from a clinical isolate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.

Halfon, Y.Jimenez-Fernandez, A.La Rosa, R.Espinosa Portero, R.Krogh Johansen, H.Matzov, D.Eyal, Z.Bashan, A.Zimmerman, E.Belousoff, M.Molin, S.Yonath, A.

(2019) Proc Natl Acad Sci U S A 116: 22275-22281

  • DOI: https://doi.org/10.1073/pnas.1909831116
  • Primary Citation of Related Structures:  
    6SPB, 6SPC, 6SPD, 6SPE, 6SPF, 6SPG

  • PubMed 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 major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa 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.


  • Organizational Affiliation

    Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]239Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]205Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A140S919 (Pseudomonas aeruginosa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]205Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]156Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]105Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A069Q263 (Pseudomonas aeruginosa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]154Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]129Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]126Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]96Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]115Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]121Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]110Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth n]98Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]86Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]78Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A2V4FRZ2 (Pseudomonas aeruginosa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]76Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]71Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A2V3DLV3 (Pseudomonas aeruginosa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]80Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]85Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A072ZDZ9 (Pseudomonas aeruginosa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth u]63Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth C]271Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth D]207Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A072ZBZ2 (Pseudomonas aeruginosa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth E]199Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A241XH26 (Pseudomonas aeruginosa)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth F]174Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A072ZMU2 (Pseudomonas aeruginosa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth G]173Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A2V3F3S9 (Pseudomonas aeruginosa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth H]78Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11DA [auth I]140Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth J]141Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth K]120Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth L]143Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A2V3D5Z8 (Pseudomonas aeruginosa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth M]135Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth N]118Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth O]115Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth P]113Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth Q]117Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth R]102Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth S]109Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth T]92Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth U]103Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25QA [auth V]188Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth W]76Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28SA [auth X]77Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL29TA [auth Y]60Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30UA [auth Z]57Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31VA [auth 1]31Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32WA [auth 2]53Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A069QB25 (Pseudomonas aeruginosa)
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UniProt GroupA0A069QB25
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33XA [auth 3]50Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A140SG33 (Pseudomonas aeruginosa)
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UniProt GroupA0A140SG33
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34YA [auth 4]44Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A087L9L7 (Pseudomonas aeruginosa)
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UniProt GroupA0A087L9L7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35ZA [auth 5]63Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A069QC44 (Pseudomonas aeruginosa)
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UniProt GroupA0A069QC44
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36AB [auth 6]38Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for E2RXU2 (Pseudomonas aeruginosa)
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UniProt GroupE2RXU2
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth a]1,526Pseudomonas aeruginosa
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S ribosomal RNAV [auth A]2,888Pseudomonas aeruginosa
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S ribosomal RNAW [auth B]117Pseudomonas aeruginosa
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
BB [auth a],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
CB [auth a],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
DB [auth a],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
EB [auth a],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
FB [auth a],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
GB [auth a],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
HB [auth a],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
IB [auth a],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
JB [auth a],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
KB [auth a],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
LB [auth a],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
MB [auth a],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
NB [auth a],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
OB [auth a],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth B],
PB [auth a],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth D],
QB [auth a],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth P],
RB [auth a],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmarkDFF-4181-00115
Novo Nordisk FoundationDenmark--
European Research Council322581
European UnioniNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references