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 

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This is version 1.2 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: https://doi.org/10.1038/nsmb1150
  • Primary Citation of Related Structures:  
    4V4H

  • 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 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3B [auth AC],
BB [auth CC]
233Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4C [auth AD],
CB [auth CD]
206Escherichia coliMutation(s): 0 
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Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5D [auth AE],
DB [auth CE]
167Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6E [auth AF],
EB [auth CF]
135Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7F [auth AG],
FB [auth CG]
179Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8G [auth AH],
GB [auth CH]
130Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9H [auth AI],
HB [auth CI]
130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10I [auth AJ],
IB [auth CJ]
103Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11J [auth AK],
JB [auth CK]
129Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12K [auth AL],
KB [auth CL]
124Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13L [auth AM],
LB [auth CM]
118Escherichia coliMutation(s): 0 
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Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14M [auth AN],
MB [auth CN]
101Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15N [auth AO],
NB [auth CO]
89Escherichia coliMutation(s): 0 
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Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16O [auth AP],
OB [auth CP]
82Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17P [auth AQ],
PB [auth CQ]
84Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18Q [auth AR],
QB [auth CR]
75Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19R [auth AS],
RB [auth CS]
92Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20S [auth AT],
SB [auth CT]
87Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2T [auth AB],
TB [auth CB]
241Escherichia coliMutation(s): 0 
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Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S21U [auth AU],
UB [auth CU]
71Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25X [auth BV],
XB [auth DV]
94Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2Y [auth BC],
YB [auth DC]
273Escherichia coliMutation(s): 0 
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Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3Z [auth BD],
ZB [auth DD]
209Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4AA [auth BE],
AC [auth DE]
201Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5BA [auth BF],
BC [auth DF]
179Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6CA [auth BG],
CC [auth DG]
177Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9DA [auth BH],
DC [auth DH]
149Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13EA [auth BJ],
EC [auth DJ]
142Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14FA [auth BK],
FC [auth DK]
123Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15GA [auth BL],
GC [auth DL]
144Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16HA [auth BM],
HC [auth DM]
136Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17IA [auth BN],
IC [auth DN]
127Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18JA [auth BO],
JC [auth DO]
117Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19KA [auth BP],
KC [auth DP]
115Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20LA [auth BQ],
LC [auth DQ]
118Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21MA [auth BR],
MC [auth DR]
103Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22NA [auth BS],
NC [auth DS]
110Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23OA [auth BT],
OC [auth DT]
100Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24PA [auth BU],
PC [auth DU]
104Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27QA [auth BW],
QC [auth DW]
85Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29RA [auth BX],
RC [auth DX]
63Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30SA [auth BY],
SC [auth DY]
59Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31TA [auth BZ],
TC [auth DZ]
70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32UA [auth B0],
UC [auth D0]
57Escherichia coliMutation(s): 0 
UniProt
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UniProt GroupP0A7N4
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33VA [auth B1],
VC [auth D1]
55Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34WA [auth B2],
WC [auth D2]
46Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35XA [auth B3],
XC [auth D3]
65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36YA [auth B4],
YC [auth D4]
38Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11ZA [auth BI],
ZC [auth DI]
142Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNAA [auth AA],
AB [auth CA]
1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAV [auth BA],
VB [auth DA]
120Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAW [auth BB],
WB [auth DB]
2,904Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KSG
Query on KSG

Download Ideal Coordinates CCD File 
AD [auth AA],
PJ [auth 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
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth BB]
AH [auth BB]
AI [auth BB]
AE [auth AA],
AF [auth AA],
AG [auth BB],
AH [auth BB],
AI [auth BB],
AJ [auth BB],
AK [auth CA],
AL [auth CA],
AM [auth DB],
AN [auth DB],
AO [auth DB],
AP [auth DB],
AQ [auth DB],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth BB],
BH [auth BB],
BI [auth BB],
BJ [auth BB],
BK [auth CA],
BL [auth CA],
BM [auth DB],
BN [auth DB],
BO [auth DB],
BP [auth DB],
BQ [auth DB],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BB],
CH [auth BB],
CI [auth BB],
CJ [auth BB],
CK [auth CA],
CL [auth CA],
CM [auth DB],
CN [auth DB],
CO [auth DB],
CP [auth DB],
CQ [auth DB],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BB],
DH [auth BB],
DI [auth BB],
DJ [auth BB],
DK [auth CA],
DL [auth CA],
DM [auth DB],
DN [auth DB],
DO [auth DB],
DP [auth DB],
DQ [auth DB],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BB],
EH [auth BB],
EI [auth BB],
EJ [auth BB],
EK [auth CA],
EL [auth CA],
EM [auth DB],
EN [auth DB],
EO [auth DB],
EP [auth DB],
EQ [auth DB],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BB],
FH [auth BB],
FI [auth BB],
FJ [auth BB],
FK [auth CA],
FL [auth CA],
FM [auth DB],
FN [auth DB],
FO [auth DB],
FP [auth DB],
FQ [auth DE],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BB],
GH [auth BB],
GI [auth BB],
GJ [auth BB],
GK [auth CA],
GL [auth CA],
GM [auth DB],
GN [auth DB],
GO [auth DB],
GP [auth DB],
GQ [auth DN],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BB],
HH [auth BB],
HI [auth BB],
HJ [auth BB],
HK [auth CA],
HL [auth CA],
HM [auth DB],
HN [auth DB],
HO [auth DB],
HP [auth DB],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BB],
IH [auth BB],
II [auth BB],
IJ [auth BB],
IK [auth CA],
IL [auth CA],
IM [auth DB],
IN [auth DB],
IO [auth DB],
IP [auth DB],
JD [auth AA],
JE [auth AA],
JF [auth BB],
JG [auth BB],
JH [auth BB],
JI [auth BB],
JJ [auth BB],
JK [auth CA],
JL [auth CA],
JM [auth DB],
JN [auth DB],
JO [auth DB],
JP [auth DB],
KD [auth AA],
KE [auth AA],
KF [auth BB],
KG [auth BB],
KH [auth BB],
KI [auth BB],
KJ [auth BB],
KK [auth CA],
KL [auth CA],
KM [auth DB],
KN [auth DB],
KO [auth DB],
KP [auth DB],
LD [auth AA],
LE [auth AA],
LF [auth BB],
LG [auth BB],
LH [auth BB],
LI [auth BB],
LJ [auth BB],
LK [auth CA],
LL [auth CA],
LM [auth DB],
LN [auth DB],
LO [auth DB],
LP [auth DB],
MD [auth AA],
ME [auth AA],
MF [auth BB],
MG [auth BB],
MH [auth BB],
MI [auth BB],
MJ [auth BB],
MK [auth CA],
ML [auth CA],
MM [auth DB],
MN [auth DB],
MO [auth DB],
MP [auth DB],
ND [auth AA],
NE [auth AA],
NF [auth BB],
NG [auth BB],
NH [auth BB],
NI [auth BB],
NJ [auth BB],
NK [auth CA],
NL [auth CA],
NM [auth DB],
NN [auth DB],
NO [auth DB],
NP [auth DB],
OD [auth AA],
OE [auth AA],
OF [auth BB],
OG [auth BB],
OH [auth BB],
OI [auth BB],
OJ [auth BB],
OK [auth CA],
OL [auth CA],
OM [auth DB],
ON [auth DB],
OO [auth DB],
OP [auth DB],
PD [auth AA],
PE [auth AA],
PF [auth BB],
PG [auth BB],
PH [auth BB],
PI [auth BB],
PK [auth CA],
PL [auth CA],
PM [auth DB],
PN [auth DB],
PO [auth DB],
PP [auth DB],
QD [auth AA],
QE [auth AA],
QF [auth BB],
QG [auth BB],
QH [auth BB],
QI [auth BB],
QJ [auth CA],
QK [auth CA],
QL [auth CA],
QM [auth DB],
QN [auth DB],
QO [auth DB],
QP [auth DB],
RD [auth AA],
RE [auth AA],
RF [auth BB],
RG [auth BB],
RH [auth BB],
RI [auth BB],
RJ [auth CA],
RK [auth CA],
RL [auth CA],
RM [auth DB],
RN [auth DB],
RO [auth DB],
RP [auth DB],
SD [auth AA],
SE [auth AA],
SF [auth BB],
SG [auth BB],
SH [auth BB],
SI [auth BB],
SJ [auth CA],
SK [auth CA],
SL [auth CA],
SM [auth DB],
SN [auth DB],
SO [auth DB],
SP [auth DB],
TD [auth AA],
TE [auth AA],
TF [auth BB],
TG [auth BB],
TH [auth BB],
TI [auth BB],
TJ [auth CA],
TK [auth CA],
TL [auth CA],
TM [auth DB],
TN [auth DB],
TO [auth DB],
TP [auth DB],
UD [auth AA],
UE [auth AA],
UF [auth BB],
UG [auth BB],
UH [auth BB],
UI [auth BB],
UJ [auth CA],
UK [auth CA],
UL [auth CA],
UM [auth DB],
UN [auth DB],
UO [auth DB],
UP [auth DB],
VD [auth AA],
VE [auth AA],
VF [auth BB],
VG [auth BB],
VH [auth BB],
VI [auth BB],
VJ [auth CA],
VK [auth CA],
VL [auth CA],
VM [auth DB],
VN [auth DB],
VO [auth DB],
VP [auth DB],
WD [auth AA],
WE [auth AA],
WF [auth BB],
WG [auth BB],
WH [auth BB],
WI [auth BB],
WJ [auth CA],
WK [auth CA],
WL [auth CA],
WM [auth DB],
WN [auth DB],
WO [auth DB],
WP [auth DB],
XD [auth AA],
XE [auth AA],
XF [auth BB],
XG [auth BB],
XH [auth BB],
XI [auth BB],
XJ [auth CA],
XK [auth CA],
XL [auth CA],
XM [auth DB],
XN [auth DB],
XO [auth DB],
XP [auth DB],
YD [auth AA],
YE [auth AA],
YF [auth BB],
YG [auth BB],
YH [auth BB],
YI [auth BB],
YJ [auth CA],
YK [auth CA],
YL [auth CA],
YM [auth DB],
YN [auth DB],
YO [auth DB],
YP [auth DB],
ZD [auth AA],
ZE [auth AA],
ZF [auth BB],
ZG [auth BB],
ZH [auth BB],
ZI [auth BB],
ZJ [auth CA],
ZK [auth CA],
ZL [auth CA],
ZM [auth DB],
ZN [auth DB],
ZO [auth DB],
ZP [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description