4V4H

Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of kasugamycin inhibition of translation.

Schuwirth, B.S.Day, J.M.Hau, C.W.Janssen, G.R.Dahlberg, A.E.Cate, J.H.D.Vila-Sanjurjo, A.

(2006) Nat Struct Mol Biol 13: 879-886

  • DOI: 10.1038/nsmb1150
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug ...

    The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites).


    Organizational Affiliation

    Departments of Molecular and Cell Biology and Chemistry, University of California, Berkeley, California 94720, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
AE, CE
167Escherichia coliMutation(s): 0 
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
AF, CF
135Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
AG, CG
179Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
AH, CH
130Escherichia coliMutation(s): 0 
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
AK, CK
129Escherichia coliMutation(s): 0 
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
AL, CL
124Escherichia coliMutation(s): 0 
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
AN, CN
101Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
AO, CO
89Escherichia coliMutation(s): 0 
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
AR, CR
75Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
AS, CS
92Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S21
AU, CU
71Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
BC, DC
273Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
BD, DD
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
BE, DE
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
BG, DG
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L9
BH, DH
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
BJ, DJ
142Escherichia coliMutation(s): 0 
Find proteins for P0AA13 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
BM, DM
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L17
BN, DN
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L21
BR, DR
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
BU, DU
104Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L27
BW, DW
85Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L31
BZ, DZ
70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L32
B0, D0
57Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L34
B2, D2
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
AM, CM
118Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
AP, CP
82Escherichia coliMutation(s): 0 
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
AQ, CQ
84Escherichia coliMutation(s): 0 
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
AT, CT
87Escherichia coliMutation(s): 0 
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
AC, CC
233Escherichia coliMutation(s): 0 
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
AB, CB
241Escherichia coliMutation(s): 0 
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
BV, DV
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
BF, DF
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
AD, CD
206Escherichia coliMutation(s): 0 
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
BK, DK
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
BL, DL
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
BO, DO
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
BP, DP
115Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L20
BQ, DQ
118Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
BS, DS
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
BT, DT
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
BX, DX
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
BY, DY
59Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L33
B1, D1
55Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L35
B3, D3
65Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L36
B4, D4
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
BI, DI
142Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
AI, CI
130Escherichia coliMutation(s): 0 
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
AJ, CJ
103Escherichia coliMutation(s): 0 
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNAAA, CA1542Escherichia coli

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Entity ID: 22
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNABA, DA120Escherichia coli

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Entity ID: 23
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNABB, DB2904Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSG
Query on KSG

Download CCD File 
AA, CA
(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE
C14 H25 N3 O9
PVTHJAPFENJVNC-MHRBZPPQSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
AA, BB, CA, DB, DE, DN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.848α = 90
b = 379.202β = 90
c = 739.283γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other