6WQQ

Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, radezolid

  • Classification: RIBOSOME
  • Organism(s): Staphylococcus aureus
  • Mutation(s): Yes 

  • Deposited: 2020-04-29 Released: 2020-06-03 
  • Deposition Author(s): Belousoff, M.J.
  • Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

CryoEM survey of oxazolodinone antibiotics in complex with the 50S subunit of the methicillin resistant Staphylococcus aureus ribosome

Wright, A.Deane-Alder, K.Marschall, E.Bamert, R.Venugopal, H.Lithgow, T.Lupton, D.Belousoff, M.J.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
C
118Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077VMP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VMP6
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
N
57Staphylococcus aureusMutation(s): 1 
Gene Names: 
Find proteins for A0A077UWR7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UWR7
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
R
37Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
I
85Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077ULC5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077ULC5
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
A
116Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UVB6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UVB6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
K
72Staphylococcus aureusMutation(s): 0 
Gene Names: rpmCCSC87_15460
Find proteins for A0A2S6DIY7 (Staphylococcus aureus)
Go to UniProtKB:  A0A2S6DIY7
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
L
217Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8U3W0 (Staphylococcus aureus)
Go to UniProtKB:  W8U3W0
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
M
58Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8UVN7 (Staphylococcus aureus)
Go to UniProtKB:  W8UVN7
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
O
49Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UXT4 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UXT4
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
P
50Staphylococcus aureusMutation(s): 0 
Find proteins for T1YD75 (Staphylococcus aureus subsp. aureus CN1)
Go to UniProtKB:  T1YD75
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Q
65Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UL47 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UL47
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
S
207Staphylococcus aureusMutation(s): 0 
Gene Names: rplDERS072840_01155GO677_05710SAMEA1469884_01255SAMEA1531680_01596SAMEA1531701_01537SAST44_02510SAST45_02495
Find proteins for A0A166DK89 (Staphylococcus aureus)
Go to UniProtKB:  A0A166DK89
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
V
145Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8TUE6 (Staphylococcus aureus)
Go to UniProtKB:  W8TUE6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
277Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077W1J0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077W1J0
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
W
122Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UUA0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UUA0
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
X
146Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UGA7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGA7
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Y
144Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077V4G0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V4G0
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Z
122Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077UG91 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UG91
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
a
119Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
D
105Staphylococcus aureusMutation(s): 0 
Find proteins for A0A0E0VQU6 (Staphylococcus aureus subsp. aureus 71193)
Go to UniProtKB:  A0A0E0VQU6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
E
117Staphylococcus aureusMutation(s): 1 
Gene Names: 
Find proteins for A0A077UKF9 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKF9
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
F
91Staphylococcus aureusMutation(s): 1 
Gene Names: 
Find proteins for W8TUB4 (Staphylococcus aureus)
Go to UniProtKB:  W8TUB4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
G
105Staphylococcus aureusMutation(s): 1 
Gene Names: 
Find proteins for W8TRD5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRD5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
H
107Staphylococcus aureusMutation(s): 0 
Gene Names: rplYNCTC7878_00039
Find proteins for A0A2X2JWH5 (Staphylococcus aureus)
Go to UniProtKB:  A0A2X2JWH5
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
J
62Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A077URJ8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077URJ8
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Entity ID: 25
MoleculeChainsLengthOrganism
23S rRNA12923Staphylococcus aureus

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Entity ID: 26
MoleculeChainsLengthOrganism
5S rRNA2115Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RD8
Query on RD8

Download CCD File 
1
Radezolid
C22 H23 F N6 O3
BTTNOGHPGJANSW-IBGZPJMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-29 
  • Released Date: 2020-06-03 
  • Deposition Author(s): Belousoff, M.J.

Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH1910126

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release