4V56

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 
    0.311 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.220 (DCC) 

Starting Models: experimental
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Literature

A steric block in translation caused by the antibiotic spectinomycin.

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

(2007) ACS Chem Biol 2: 545-552

  • DOI: https://doi.org/10.1021/cb700100n
  • Primary Citation of Related Structures:  
    4V56, 4V57

  • PubMed Abstract: 

    The widely used antibiotic spectinomycin inhibits bacterial protein synthesis by blocking translocation of messenger RNA and transfer RNAs on the ribosome. Here, we show that in crystals of the Escherichia coli 70S ribosome spectinomycin binding traps a distinct swiveling state of the head domain of the small ribosomal subunit. Spectinomycin also alters the rate and completeness of reverse translocation in vitro. These structural and biochemical data indicate that in solution spectinomycin sterically blocks swiveling of the head domain of the small ribosomal subunit and thereby disrupts the translocation cycle.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC],
MB [auth CC]		232Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4BB [auth CD],
C [auth AD]		205Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5CB [auth CE],
D [auth AE]		166Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6DB [auth CF],
E [auth AF]		135Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG],
NB [auth CG]		178Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8EB [auth CH],
G [auth AH]		129Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI],
OB [auth CI]		129Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth AJ],
PB [auth CJ]		103Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11FB [auth CK],
J [auth AK]		128Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12GB [auth CL],
K [auth AL]		123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM],
QB [auth CM]		117Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16HB [auth CP],
M [auth AP]		82Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17IB [auth CQ],
N [auth AQ]		83Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18JB [auth CR],
O [auth AR]		74Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19P [auth AS],
SB [auth CS]		91Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20KB [auth CT],
Q [auth AT]		86Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2R [auth AB],
TB [auth CB]		240Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21LB [auth CU],
S [auth AU]		70Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15T [auth AO],
UB [auth CO]		89Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RB [auth CN],
U [auth AN]		100Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11X [auth BI],
XB [auth DI]		141Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth BC],
YB [auth DC]		272Escherichia 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 L14AA [auth BK],
AC [auth DK]		123Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19BA [auth BP],
BC [auth DP]		114Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth BE],
CC [auth DE]		201Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth BY],
DC [auth DY]		58Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EA [auth B0],
EC [auth D0]		56Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth B4],
FC [auth D4]		38Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GA [auth B1],
GC [auth D1]		54Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35HA [auth B3],
HC [auth D3]		64Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25IA [auth BV],
IC [auth DV]		94Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34JA [auth B2],
JC [auth D2]		46Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth BL],
KC [auth DL]		144Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth BM],
LC [auth DM]		136Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29MA [auth BX],
MC [auth DX]		63Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9NA [auth BH],
NC [auth DH]		149Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13OA [auth BJ],
OC [auth DJ]		142Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17PA [auth BN],
PC [auth DN]		127Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18QA [auth BO],
QC [auth DO]		117Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth BQ],
RC [auth DQ]		117Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth BS],
SC [auth DS]		110Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth BU],
TC [auth DU]		103Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5UA [auth BF],
UC [auth DF]		178Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6VA [auth BG],
VC [auth DG]		176Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21WA [auth BR],
WC [auth DR]		103Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23XA [auth BT],
XC [auth DT]		100Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth BZ],
YC [auth DZ]		78Escherichia coliMutation(s): 0 
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Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27ZA [auth BW],
ZC [auth DW]		84Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SCM
Query on SCM
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IF [auth AA],
WL [auth CA]		SPECTINOMYCIN
C14 H24 N2 O7
UNFWWIHTNXNPBV-WXKVUWSESA-N
ZN
Query on ZN
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EQ [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free:  0.311 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.220 (DCC) 
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
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SCMClick on this verticalbar to view details

View more in-depth experimental data
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, Structure summary