6S13

Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 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

Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.

Halfon, Y.Matzov, D.Eyal, Z.Bashan, A.Zimmerman, E.Kjeldgaard, J.Ingmer, H.Yonath, A.

(2019) Sci Rep 9: 11460-11460

  • DOI: 10.1038/s41598-019-48019-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms ...

    The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.


    Organizational Affiliation

    National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Kgs, Lyngby, Denmark.,The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark.,The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel. ada.yonath@weizmann.ac.il.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
274Staphylococcus aureusMutation(s): 0 
Gene Names: rap (rplB)
Find proteins for B3VKN3 (Staphylococcus aureus)
Go to UniProtKB:  B3VKN3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
215Staphylococcus aureusMutation(s): 0 
Gene Names: rplC (rplC_1)
Find proteins for W8U3W0 (Staphylococcus aureus)
Go to UniProtKB:  W8U3W0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
206Staphylococcus aureusMutation(s): 0 
Gene Names: rplD (rplD_1)
Find proteins for W8TRC7 (Staphylococcus aureus)
Go to UniProtKB:  W8TRC7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
175Staphylococcus aureusMutation(s): 0 
Gene Names: rplE (rplE_1)
Find proteins for W8TUC3 (Staphylococcus aureus)
Go to UniProtKB:  W8TUC3
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
175Staphylococcus aureusMutation(s): 0 
Gene Names: rplF_1 (rplF)
Find proteins for W8U3X2 (Staphylococcus aureus)
Go to UniProtKB:  W8U3X2
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
H
145Staphylococcus aureusMutation(s): 0 
Gene Names: rplM (rplM_1, rplM_2, rplM_3, rplM_4)
Find proteins for W8TUE6 (Staphylococcus aureus)
Go to UniProtKB:  W8TUE6
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
I
122Staphylococcus aureusMutation(s): 0 
Gene Names: rplN (rplN_1, rplNA)
Find proteins for A0A077UUA0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UUA0
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
J
146Staphylococcus aureusMutation(s): 0 
Gene Names: rplO (rplO_1)
Find proteins for A0A077UGA7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGA7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
137Staphylococcus aureusMutation(s): 0 
Gene Names: rplP (rplP_1)
Find proteins for A0A077V4G0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V4G0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
L
120Staphylococcus aureusMutation(s): 0 
Gene Names: rplQ (rplQ_1, rplQ_2)
Find proteins for A0A077UG91 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UG91
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
M
119Staphylococcus aureusMutation(s): 0 
Gene Names: rplR_1 (rplR)
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
N
114Staphylococcus aureusMutation(s): 0 
Gene Names: rplS (rplS_1)
Find proteins for A0A077UVB6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UVB6
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
O
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplT (rplT_2)
Find proteins for A0A077VMP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VMP6
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
P
102Staphylococcus aureusMutation(s): 0 
Gene Names: rplU
Find proteins for D7URR3 (Staphylococcus aureus)
Go to UniProtKB:  D7URR3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
110Staphylococcus aureusMutation(s): 0 
Gene Names: rplV (rplV_1)
Find proteins for A0A077UKF9 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKF9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
R
89Staphylococcus aureusMutation(s): 0 
Gene Names: rplW (rplW_1)
Find proteins for W8TUB4 (Staphylococcus aureus)
Go to UniProtKB:  W8TUB4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
S
103Staphylococcus aureusMutation(s): 0 
Gene Names: rplX (rplX_1)
Find proteins for W8TRD5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRD5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
T
94Staphylococcus aureusMutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
Go to UniProtKB:  A0A133Q8Z9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
82Staphylococcus aureusMutation(s): 0 
Gene Names: rpmA (rpmA_1)
Find proteins for A0A077ULC5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077ULC5
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
V
58Staphylococcus aureusMutation(s): 0 
Gene Names: rpmB (rpmB_1)
Find proteins for A0A077URJ8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077URJ8
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
W
67Staphylococcus aureusMutation(s): 0 
Gene Names: rpmC (rpmC_1)
Find proteins for A0A077W1J5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077W1J5
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
X
58Staphylococcus aureusMutation(s): 0 
Gene Names: rpmD (rpmD_1)
Find proteins for W8UVN7 (Staphylococcus aureus)
Go to UniProtKB:  W8UVN7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
Y
59Staphylococcus aureusMutation(s): 0 
Gene Names: rpmE2
Find proteins for A0A380EL30 (Staphylococcus aureus)
Go to UniProtKB:  A0A380EL30
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Z
48Staphylococcus aureusMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A1Q8DAT0 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q8DAT0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
47Staphylococcus aureusMutation(s): 0 
Gene Names: rpmG2 (rpmG, rpmG_1, rpmGA)
Find proteins for A0A077V2P0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V2P0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
43Staphylococcus aureusMutation(s): 0 
Gene Names: rpmH (rpmH_1)
Find proteins for W8TQ59 (Staphylococcus aureus)
Go to UniProtKB:  W8TQ59
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Staphylococcus aureusMutation(s): 0 
Gene Names: rpmI (rpmI_2)
Find proteins for A0A077UL47 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UL47
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Staphylococcus aureusMutation(s): 0 
Gene Names: rpmJ (rpmJ_1)
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
226Staphylococcus aureusMutation(s): 0 
Gene Names: rpsB
Find proteins for A0A2X2M020 (Staphylococcus aureus)
Go to UniProtKB:  A0A2X2M020
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
202Staphylococcus aureusMutation(s): 0 
Gene Names: rpsC (rpsC_1)
Find proteins for A0A077UU26 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UU26
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
198Staphylococcus aureusMutation(s): 0 
Gene Names: rpsD_2 (rpsD)
Find proteins for W8TVK2 (Staphylococcus aureus)
Go to UniProtKB:  W8TVK2
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
156Staphylococcus aureusMutation(s): 0 
Gene Names: rpsE (rpsE_1)
Find proteins for W8TUC9 (Staphylococcus aureus)
Go to UniProtKB:  W8TUC9
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
95Staphylococcus aureusMutation(s): 0 
Gene Names: rpsF (rpsF_1, rpsF_2, rpsF_3, rpsF_4)
Find proteins for W8TPC6 (Staphylococcus aureus)
Go to UniProtKB:  W8TPC6
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
152Staphylococcus aureusMutation(s): 0 
Gene Names: rpsG (rpsG_1)
Find proteins for A0A077VHU6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VHU6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
131Staphylococcus aureusMutation(s): 0 
Gene Names: rpsH (rpsH_1)
Find proteins for W8U8T8 (Staphylococcus aureus)
Go to UniProtKB:  W8U8T8
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
127Staphylococcus aureusMutation(s): 0 
Gene Names: rpsI
Find proteins for A0A1Q4GY48 (Staphylococcus aureus)
Go to UniProtKB:  A0A1Q4GY48
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
97Staphylococcus aureusMutation(s): 0 
Gene Names: rpsJ (rpsJ_1)
Find proteins for A0A0H2K0A0 (Staphylococcus aureus)
Go to UniProtKB:  A0A0H2K0A0
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
114Staphylococcus aureusMutation(s): 0 
Gene Names: rpsK (rpsK_1, rpsK_2)
Find proteins for A0A077UKD6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKD6
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
135Staphylococcus aureusMutation(s): 0 
Gene Names: rpsL
Find proteins for A0A133PZQ5 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PZQ5
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
104Staphylococcus aureusMutation(s): 0 
Gene Names: rpsM (rpsM_1)
Find proteins for W8U8U6 (Staphylococcus aureus)
Go to UniProtKB:  W8U8U6
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
60Staphylococcus aureusMutation(s): 0 
Gene Names: rpsN_1 (rpsN, rpsN_2, rpsNA, rpsZ)
Find proteins for A0A077UGW7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGW7
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
88Staphylococcus aureusMutation(s): 0 
Gene Names: rpsO (rpsO_1)
Find proteins for W8U6H8 (Staphylococcus aureus)
Go to UniProtKB:  W8U6H8
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
89Staphylococcus aureusMutation(s): 0 
Gene Names: rpsP (rpsP_1)
Find proteins for W8U6K4 (Staphylococcus aureus)
Go to UniProtKB:  W8U6K4
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsQ (rpsQ_1)
Find proteins for A0A077VLD5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VLD5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
54Staphylococcus aureusMutation(s): 0 
Gene Names: rpsR (rpsR_1, rpsR_2, rpsR_3, rpsR_4)
Find proteins for A0A077UZF4 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UZF4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
80Staphylococcus aureusMutation(s): 0 
Gene Names: rpsS
Find proteins for A0A133PYC3 (Staphylococcus aureus)
Go to UniProtKB:  A0A133PYC3
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
81Staphylococcus aureusMutation(s): 0 
Gene Names: rpsT (rpsT_1)
Find proteins for W8UXC3 (Staphylococcus aureus)
Go to UniProtKB:  W8UXC3
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
52Staphylococcus aureusMutation(s): 0 
Gene Names: rpsU
Find proteins for A0A380DEA2 (Staphylococcus aureus)
Go to UniProtKB:  A0A380DEA2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promoting factor
v
162Staphylococcus aureusMutation(s): 0 
Gene Names: hpf (raiA, yfiA)
Find proteins for W8USK0 (Staphylococcus aureus)
Go to UniProtKB:  W8USK0
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2905Staphylococcus aureus
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB115Staphylococcus aureus
Entity ID: 31
MoleculeChainsLengthOrganism
16S ribosomal RNAa1539Staphylococcus aureus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council322581
Danish National Research FoundationDenmark--

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release