2QEX

Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.

Schroeder, S.J.Blaha, G.Moore, P.B.

(2007) Antimicrob Agents Chemother 51: 4462-4465

  • DOI: 10.1128/AAC.00455-07
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of a ...

    Negamycin, a small-molecule inhibitor of protein synthesis, binds the Haloarcula marismortui 50S ribosomal subunit at a single site formed by highly conserved RNA nucleotides near the cytosolic end of the nascent chain exit tunnel. The mechanism of antibiotic action and the function of this unexplored tunnel region remain intriguingly elusive.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2P
A
240Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20276

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3P
B
338Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4P
C
246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5P
D
177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6P
E
178Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14135

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
F
120Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12743

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Acidic ribosomal protein P0 homolog
G
348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P15825

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10e
H
174Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60617

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13P
J
145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14P
K
132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22450

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15P
L
165Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15e
M
196Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60618

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P
N
187Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18e
O
116Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12733

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19e
P
149Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14119

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21e
Q
96Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12734

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22P
R
155Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10970

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23P
S
85Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24P
T
120Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24e
U
67Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29P
V
71Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30P
W
154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14121

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31e
X
92Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P18138

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32e
Y
241Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12736

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37Ae
Z
73Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60619

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e
1
57Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32410

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e
2
50Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22452

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44e
3
92Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32411

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11P
I
162Haloarcula marismortuiMutation(s): 0 
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14122

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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA02772Haloarcula marismortui

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA9122Haloarcula marismortui
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEG
Query on NEG

Download CCD File 
0
NEGAMYCIN
C9 H20 N4 O4
IKHFJPZQZVMLRH-RNFRBKRXSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
0, 3, A, B, J, L, M, N, O, Q, R
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
0, 3, 9, A, B, K, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
0, 9, A, C, H, J, L, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.62α = 90
b = 304.048β = 90
c = 578.647γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Database references
  • Version 1.3: 2017-10-18
    Changes: Refinement description