8CVM

Cutibacterium acnes 50S ribosomal subunit with P-site tRNA and Sarecycline bound in the local refined map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 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

Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.

Lomakin, I.B.Devarkar, S.C.Patel, S.Grada, A.Bunick, C.G.

(2023) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkad103
  • Primary Citation of Related Structures:  
    8CRX, 8CVM, 8CVO, 8CWO

  • PubMed Abstract: 
  • Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy ...

    Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.


    Related Citations: 
    • The structure of the Cutibacterium acnes 70S ribosome
      Lomakin, I.B., Devarkar, S.C., Grada, A., Bunick, C.G.
      () To be published --: --

    Organizational Affiliation

    Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth c]278Cutibacterium acnesMutation(s): 0 
Gene Names: rplBCOH10_09965
UniProt
Find proteins for A0A2B7JMV5 (Cutibacterium acnes)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth d]223Cutibacterium acnesMutation(s): 0 
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Find proteins for A0A085B5E3 (Cutibacterium acnes HL201PA1)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth e]301Cutibacterium acnesMutation(s): 0 
Gene Names: rplDCOH10_09975
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth f]210Cutibacterium acnesMutation(s): 0 
Gene Names: rplECOH10_09920
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth g]180Cutibacterium acnesMutation(s): 0 
Gene Names: rplFCOH10_09905
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13F [auth i]147Cutibacterium acnesMutation(s): 0 
Gene Names: rplMCOH10_09695
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14G [auth j]122Cutibacterium acnesMutation(s): 0 
Gene Names: rplNCOH10_09930
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15H [auth k]146Cutibacterium acnesMutation(s): 0 
Gene Names: rplOCOH10_09885
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Entity ID: 9
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50S ribosomal protein L16I [auth l]139Cutibacterium acnesMutation(s): 0 
Gene Names: rplPCOH10_09945
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth m]187Cutibacterium acnesMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth n]127Cutibacterium acnesMutation(s): 0 
Gene Names: rplRCOH10_09900
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth o]117Cutibacterium acnesMutation(s): 0 
Gene Names: rplSCOH10_11165
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Entity ID: 13
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50S ribosomal protein L20M [auth p]123Cutibacterium acnesMutation(s): 0 
Gene Names: rplTCOH10_11040
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth q]102Cutibacterium acnesMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22O [auth r]153Cutibacterium acnesMutation(s): 0 
Gene Names: rplVCOH10_09955
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23P [auth s]102Cutibacterium acnesMutation(s): 0 
Gene Names: rplWCOH10_09970
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth t]122Cutibacterium acnesMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25R [auth u]205Cutibacterium acnesMutation(s): 0 
Gene Names: rplYctcCOH10_04035
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27S [auth v]89Cutibacterium acnesMutation(s): 0 
Gene Names: rpmACOH10_02465
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Find proteins for A0A2B7IGT1 (Cutibacterium acnes)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28T [auth w]61Cutibacterium acnesMutation(s): 0 
Gene Names: rpmBCOH10_11380
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29U [auth x]77Cutibacterium acnesMutation(s): 0 
Gene Names: rpmCCOH10_09940DI580_10840
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Find proteins for A0A2B7JB12 (Cutibacterium acnes)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30V [auth y]60Cutibacterium acnesMutation(s): 0 
Gene Names: rpmDCOH10_09890
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32W [auth z]63Cutibacterium acnesMutation(s): 0 
Gene Names: rpmFCOH10_11270
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33X [auth 0]56Cutibacterium acnesMutation(s): 0 
Gene Names: rpmGCOH10_10145DI580_09850
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34Y [auth 1]44Cutibacterium acnesMutation(s): 0 
Gene Names: rpmHCOH10_06940DI580_06020
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35Z [auth 2]68Cutibacterium acnesMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31AA [auth 4]69Cutibacterium acnesMutation(s): 0 
Gene Names: rpmECOH10_00275DI580_04305
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL37DA [auth V]24Cutibacterium acnesMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth 3]37Cutibacterium acnesMutation(s): 0 
Gene Names: rpmJCOH10_09825DI580_10570
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Entity ID: 28
MoleculeChainsLengthOrganismImage
23S ribosomal RNABA [auth a]3,086Cutibacterium acnes
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Entity ID: 29
MoleculeChainsLengthOrganismImage
5S ribosomal RNACA [auth b]120Cutibacterium acnes
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Entity ID: 31
MoleculeChainsLengthOrganismImage
Initiator fMet RNAEA [auth C]77Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V7A (Subject of Investigation/LOI)
Query on V7A

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RA [auth a]Sarecycline
C24 H29 N3 O8
PQJQFLNBMSCUSH-SBAJWEJLSA-N
 Ligand Interaction
ZN
Query on ZN

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MA [auth w],
NA [auth z],
OA [auth 0],
QA [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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],
AI [auth a],
AJ [auth a],
AK [auth a],
AL [auth a],
AM [auth b],
BB [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 b],
CB [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 C],
DB [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 C],
EB [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],
FB [auth a],
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],
GA [auth c],
GB [auth a],
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],
HA [auth c],
HB [auth a],
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],
IA [auth c],
IB [auth a],
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],
JA [auth d],
JB [auth a],
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],
KA [auth k],
KB [auth a],
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],
LA [auth k],
LB [auth a],
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],
MB [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],
NB [auth a],
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],
OB [auth a],
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],
PA [auth 1],
PB [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],
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],
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],
SA [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],
TA [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],
UA [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],
VA [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],
WA [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],
XA [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],
YA [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],
ZA [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.9.6 EL
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Almirall, LLCUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release