4V64

Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.269 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for hygromycin B inhibition of protein biosynthesis

Borovinskaya, M.A., Shoji, S., Fredrick, K., Cate, J.H.D.

(2008) RNA 14: 1590-1599

  • DOI: https://doi.org/10.1261/rna.1076908
  • Primary Citation of Related Structures:  
    4V64

  • PubMed Abstract: 

    Aminoglycosides are one of the most widely used and clinically important classes of antibiotics that target the ribosome. Hygromycin B is an atypical aminoglycoside antibiotic with unique structural and functional properties. Here we describe the structure of the intact Escherichia coli 70S ribosome in complex with hygromycin B. The antibiotic binds to the mRNA decoding center in the small (30S) ribosomal subunit of the 70S ribosome and induces a localized conformational change, in contrast to its effects observed in the structure of the isolated 30S ribosomal subunit in complex with the drug. The conformational change in the ribosome caused by hygromycin B binding differs from that induced by other aminoglycosides. Also, in contrast to other aminoglycosides, hygromycin B potently inhibits spontaneous reverse translocation of tRNAs and mRNA on the ribosome in vitro. These structural and biochemical results help to explain the unique mode of translation inhibition by hygromycin B.

    • Organizational Affiliation: 

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC],
BB [auth CC]		232Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth AD],
CB [auth CD]		205Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth AE],
DB [auth CE]		166Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth AF],
EB [auth CF]		135Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG],
FB [auth CG]		178Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth AH],
GB [auth CH]		129Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI],
HB [auth CI]		129Escherichia 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]		128Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth AL],
KB [auth CL]		123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM],
LB [auth CM]		117Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14M [auth AN],
MB [auth CN]		100Escherichia 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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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]		83Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth AR],
QB [auth CR]		74Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth AS],
RB [auth CS]		91Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth AT],
SB [auth CT]		86Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2T [auth AB],
TB [auth CB]		240Escherichia coliMutation(s): 0 
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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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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]		178Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth BG],
CC [auth DG]		176Escherichia 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]		114Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth BQ],
LC [auth DQ]		117Escherichia 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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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth BT],
OC [auth DT]		100Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth BU],
PC [auth DU]		103Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth BW],
QC [auth DW]		84Escherichia 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]		58Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28TA [auth BZ],
TC [auth DZ]		78Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth B0],
UC [auth D0]		56Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth B1],
VC [auth D1]		54Escherichia coliMutation(s): 0 
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Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth B2],
WC [auth D2]		46Escherichia coliMutation(s): 0 
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Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth B3],
XC [auth D3]		64Escherichia coliMutation(s): 0 
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Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth B4],
YC [auth D4]		38Escherichia coliMutation(s): 0 
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Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11ZA [auth BI],
ZC [auth DI]		141Escherichia coliMutation(s): 0 
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Find proteins for P0A7J7 (Escherichia coli (strain K12))
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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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HYG
Query on HYG
Download Ideal Coordinates CCD File 
GF [auth AA],
ZL [auth CA]		HYGROMYCIN B
C20 H37 N3 O13
GRRNUXAQVGOGFE-WRWUMOMGSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IQ [auth D4],
PJ [auth B4]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AD [auth AA]
AE [auth AA]
AF [auth AA]
AG [auth BB]
AH [auth BB]
AD [auth AA],
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 CE],
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 DB],
GD [auth AA],
GE [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 DB],
HD [auth AA],
HE [auth AA],
HF [auth AE],
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],
HQ [auth DB],
ID [auth AA],
IE [auth AA],
IF [auth AN],
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],
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: 3.50 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.7α = 90
b = 379.5β = 90
c = 739.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary