4WOI

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.

Wasserman, M.R.Pulk, A.Zhou, Z.Altman, R.B.Zinder, J.C.Green, K.D.Garneau-Tsodikova, S.Doudna Cate, J.H.Blanchard, S.C.

(2015) Nat Commun 6: 7896-7896

  • DOI: 10.1038/ncomms8896

  • PubMed Abstract: 
  • Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we s ...

    Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.


    Organizational Affiliation

    Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, DB
241Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, DC
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, DD
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, DE
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, DF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, DG
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, DH
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, DI
130Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, DJ
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, DK
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, DL
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, DM
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, DN
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, DO
89N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, DP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, DQ
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, DR
75Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, DS
92Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, DT
87Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU, DU
71Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome-recycling factor
AV
185Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frr (rrf)
Find proteins for P0A805 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A805
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC, CC
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD, CD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE, CE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF, CF
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG, CG
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH, CH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI, CI
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ, CJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK, CK
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL, CL
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM, CM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN, CN
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO, CO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP, CP
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ, CQ
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR, CR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS, CS
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT, CT
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU, CU
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV, CV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW, CW
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BX, CX
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY, CY
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ, CZ
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B0, C0
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1, C1
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B2, C2
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B3, C3
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B4, C4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
B5
228Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA,DA1542Escherichia coli str. K-12 substr. MDS42
Entity ID: 23
MoleculeChainsLengthOrganism
Messenger RNAAW,DV16Enterobacteria phage L1
Entity ID: 24
MoleculeChainsLengthOrganism
Phenylalanine specific transfer RNA, tRNA-PheAX,DW76Escherichia coli str. K-12 substr. MDS42
Entity ID: 25
MoleculeChainsLengthOrganism
23S ribosomal RNABA,CA2904Escherichia coli str. K-12 substr. MDS42
Entity ID: 26
MoleculeChainsLengthOrganism
5S ribosomal RNABB,CB120Escherichia coli str. K-12 substr. MDS42
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B4, C4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PAR
Query on PAR

Download SDF File 
Download CCD File 
AA, BA, CA, DA
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AN, BA, BB, BL, BO, BQ, CA, CB, CD, CQ, DA, DD, DN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 212.100α = 90.00
b = 435.240β = 90.00
c = 614.440γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States2R01GM079238
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM65050
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1R01AI090048
National Institutes of Health/National Cancer InstituteUnited StatesCA92584
Human Frontiers in Science ProgramUnited StatesRGY0088
National Science Foundation (United States)United States0644129
Department of Energy (United States)United StatesDE-AC0376SF00098

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description