8CGD

Clindamycin bound to the 50S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural conservation of antibiotic interaction with ribosomes.

Paternoga, H.Crowe-McAuliffe, C.Bock, L.V.Koller, T.O.Morici, M.Beckert, B.Myasnikov, A.G.Grubmuller, H.Novacek, J.Wilson, D.N.

(2023) Nat Struct Mol Biol 30: 1380-1392

  • DOI: https://doi.org/10.1038/s41594-023-01047-y
  • Primary Citation of Related Structures:  
    8CA7, 8CAI, 8CAM, 8CAZ, 8CEP, 8CEU, 8CF1, 8CF8, 8CGD, 8CGI, 8CGJ, 8CGK, 8CGR, 8CGU, 8CGV

  • PubMed Abstract: 

    The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33A [auth 0]55Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34B [auth 1]46Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35C [auth 2]65Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36AD [auth 3]38Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2G [auth c]273Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3H [auth d]209Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4I [auth e]201Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5J [auth f]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6K [auth g]177Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9L [auth h]149Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13M [auth i]142Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14N [auth j]123Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth k]144Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16P [auth l]136Escherichia coli BW25113Mutation(s): 1 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17Q [auth m]127Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18R [auth n]117Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19S [auth o]115Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20T [auth p]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21U [auth q]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22V [auth r]110Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23W [auth s]100Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24X [auth t]104Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Y [auth u]94Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27Z [auth v]85Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28AA [auth w]78Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29BA [auth x]63Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30CA [auth y]59Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32DA [auth z]57Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 5
MoleculeChains LengthOrganismImage
23S rRNAE [auth a]2,904Escherichia coli BW25113
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Entity ID: 6
MoleculeChains LengthOrganismImage
5S rRNAF [auth b]120Escherichia coli BW25113
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AM2 (Subject of Investigation/LOI)
Query on AM2

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HA [auth a]APRAMYCIN
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
CLY (Subject of Investigation/LOI)
Query on CLY

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GA [auth a]CLINDAMYCIN
C18 H33 Cl N2 O5 S
KDLRVYVGXIQJDK-AWPVFWJPSA-N
ZN
Query on ZN

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EA [auth 3],
GN [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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FA [auth a]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

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AI [auth a]
AJ [auth a]
AK [auth a]
AN [auth c]
BI [auth a]
AI [auth a],
AJ [auth a],
AK [auth a],
AN [auth c],
BI [auth a],
BJ [auth a],
BK [auth a],
BN [auth c],
CI [auth a],
CJ [auth a],
CK [auth a],
CN [auth c],
DI [auth a],
DJ [auth a],
DK [auth a],
DN [auth c],
EI [auth a],
EJ [auth a],
EK [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FN [auth e],
GI [auth a],
GJ [auth a],
GK [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
II [auth a],
IJ [auth a],
IK [auth a],
IN [auth t],
JI [auth a],
JJ [auth a],
JK [auth a],
KI [auth a],
KJ [auth a],
KK [auth a],
LI [auth a],
LJ [auth a],
LK [auth a],
MI [auth a],
MJ [auth a],
MK [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
UM [auth a],
VH [auth a],
VI [auth a],
VJ [auth a],
WH [auth a],
WI [auth a],
WJ [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
YH [auth a],
YI [auth a],
YJ [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth a]
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth a]
AB [auth a],
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AL [auth a],
AM [auth a],
BB [auth a],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BL [auth a],
BM [auth a],
CB [auth a],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CL [auth a],
CM [auth a],
DB [auth a],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DL [auth a],
DM [auth a],
EB [auth a],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EL [auth a],
EM [auth a],
EN [auth d],
FB [auth a],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FL [auth a],
FM [auth a],
GB [auth a],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GL [auth a],
GM [auth a],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HL [auth a],
HM [auth a],
HN [auth p],
IA [auth a],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
IL [auth a],
IM [auth a],
JA [auth a],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JL [auth a],
JM [auth a],
JN [auth z],
KA [auth a],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KL [auth a],
KM [auth a],
LA [auth a],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LL [auth a],
LM [auth a],
MA [auth a],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
ML [auth a],
MM [auth a],
NA [auth a],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
NK [auth a],
NL [auth a],
NM [auth a],
OA [auth a],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
OK [auth a],
OL [auth a],
OM [auth a],
PA [auth a],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
PK [auth a],
PL [auth a],
PM [auth a],
QA [auth a],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
QK [auth a],
QL [auth a],
QM [auth a],
RA [auth a],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
RK [auth a],
RL [auth a],
RM [auth a],
SA [auth a],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
SK [auth a],
SL [auth a],
SM [auth a],
TA [auth a],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
TK [auth a],
TL [auth a],
TM [auth a],
UA [auth a],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
UK [auth a],
UL [auth a],
VA [auth a],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
VK [auth a],
VL [auth a],
VM [auth b],
WA [auth a],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
WK [auth a],
WL [auth a],
WM [auth b],
XA [auth a],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XK [auth a],
XL [auth a],
XM [auth b],
YA [auth a],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YK [auth a],
YL [auth a],
YM [auth b],
ZA [auth a],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZK [auth a],
ZL [auth a],
ZM [auth c]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ
H [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
P [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0415

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentDLR01Kl1820
iNEXT-DiscoveryEuropean Union871037
Other governmentLM2018127

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-20
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations