8R8M

70S Escherichia coli ribosome with Paenilamicin B2 bound with hybrid A/P- and hybrid P/E-tRNA.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.

Koller, T.O.Berger, M.J.Morici, M.Paternoga, H.Bulatov, T.Di Stasi, A.Dang, T.Mainz, A.Raulf, K.Crowe-McAuliffe, C.Scocchi, M.Mardirossian, M.Beckert, B.Vazquez-Laslop, N.Mankin, A.Sussmuth, R.D.Wilson, D.N.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.05.21.595107
  • Primary Citation of Related Structures:  
    8R6C, 8R8M, 9FBV

  • PubMed Abstract: 

    The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus . While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae . We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2F [auth c]273Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3G [auth d]209Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4H [auth e]201Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5I [auth f]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6J [auth g]177Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9K [auth h]149Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13L [auth i]142Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14M [auth j]123Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth k]144Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16O [auth l]136Escherichia coli BW25113Mutation(s): 1 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17P [auth m]127Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18Q [auth n]117Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19R [auth o]115Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20S [auth p]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21T [auth q]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22U [auth r]110Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23V [auth s]100Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24W [auth t]104Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth u]94Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27Y [auth v]85Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28Z [auth w]78Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29AA [auth x]63Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30BA [auth y]59Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32CA [auth z]57Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31AEA [auth 4]70Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3HA [auth C]233Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9IA [auth I]130Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10JA [auth J]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13KA [auth M]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14LA [auth N]101Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19MA [auth S]92Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth G]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2OA [auth B]241Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4PA [auth D]206Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5QA [auth E]167Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformRA [auth F]135Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8SA [auth H]130Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15TA [auth O]89Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth P]82Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17VA [auth Q]84Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18WA [auth R]75Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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UniProt GroupP0A7T7
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth T]87Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21YA [auth U]71Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11ZA [auth K]129Escherichia coli BW25113Mutation(s): 1 
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12AB [auth L]124Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Paenilamicin B2DB [auth 5]8synthetic constructMutation(s): 0 
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S ribosomal RNAE [auth b]120Escherichia coli BW25113
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Entity ID: 30
MoleculeChains LengthOrganismImage
mRNADA [auth X]10Escherichia coli BW25113
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Entity ID: 32
MoleculeChains LengthOrganismImage
23S ribosomal RNAFA [auth a]2,903Escherichia coli BW25113
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Entity ID: 33
MoleculeChains LengthOrganismImage
16S ribosomal RNAGA [auth A]1,534Escherichia coli BW25113
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Entity ID: 54
MoleculeChains LengthOrganismImage
Leucine-tRNABB [auth Z]85Escherichia coli BW25113
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Entity ID: 55
MoleculeChains LengthOrganismImage
Isoleucine-tRNACB [auth Y]76Escherichia coli BW25113
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EB [auth 3],
PB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CN [auth 5],
MB [auth d]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth a]
AG [auth a]
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth A],
CL [auth A],
CM [auth A],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth A],
DL [auth A],
DM [auth A],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth A],
EL [auth A],
EM [auth A],
FB [auth b],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth A],
FL [auth A],
FM [auth A],
GB [auth b],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth A],
GL [auth A],
GM [auth A],
HB [auth b],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth A],
HL [auth A],
HM [auth A],
IB [auth b],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth A],
IL [auth A],
IM [auth A],
JB [auth b],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth A],
JL [auth A],
JM [auth A],
KB [auth c],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth A],
KL [auth A],
KM [auth A],
LB [auth d],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth a],
LJ [auth a],
LK [auth A],
LL [auth A],
LM [auth A],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth a],
MK [auth A],
ML [auth A],
MM [auth A],
NB [auth p],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth A],
NL [auth A],
NM [auth A],
OB [auth z],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth A],
OL [auth A],
OM [auth A],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth A],
PK [auth A],
PL [auth A],
PM [auth A],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth a],
VI [auth a],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
WI [auth a],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
YI [auth a],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ
G [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
O [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
D2T
Query on D2T
AB [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SASP
YF5
Query on YF5
DB [auth 5]PEPTIDE LINKINGC10 H22 N4 O5YFZ
YFQ
Query on YFQ
DB [auth 5]L-PEPTIDE LINKINGC4 H10 N2 O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0425

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentWI3285/12-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release