1K9M

Co-crystal structure of tylosin bound to the 50S ribosomal subunit of Haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structures of four macrolide antibiotics bound to the large ribosomal subunit.

Hansen, J.L.Ippolito, J.A.Ban, N.Nissen, P.Moore, P.B.Steitz, T.A.

(2002) Mol.Cell 10: 117-128

  • Primary Citation of Related Structures:  1K8A, 1KD1, 1M1K

  • PubMed Abstract: 
  • Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit ...

    Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L2
C
239Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl2
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20276
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L3
D
337Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl3
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L4
E
246Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl4
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L5
F
176Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl5
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L6
G
177Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl6
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14135
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L7AE
H
119Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl7ae
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12743
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L10
I
348Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl10 (rpl10e, rplP0)
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P15825
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L10E
J
167Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl10e
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60617
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L13
K
145Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl13
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L14
L
132Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl14
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22450
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15
M
164Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl15
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15E
N
194Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl15e
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60618
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L18
O
186Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl18
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L18E
P
115Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl18e
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12733
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L19E
Q
148Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl19e
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14119
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L21E
R
95Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl21e
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12734
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L22
S
154Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl22
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10970
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L23
T
84Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl23p
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L24
U
119Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl24p
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L24E
V
66Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl24e
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L29
W
70Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl29p
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L30
X
154Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl30p
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14121
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L31E
Y
91Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl31e
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P18138
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L32E
Z
240Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl32e
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12736
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37Ae
1
73Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl37ae
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60619
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37E
2
56Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl37e
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32410
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L39E
3
48Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl39e
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22452
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L44E
4
92Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Gene Names: rpl44e
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32411
Entity ID: 1
MoleculeChainsLengthOrganism
23S RRNAA2922Haloarcula marismortui
Entity ID: 2
MoleculeChainsLengthOrganism
5S RRNAB122Haloarcula marismortui
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, E, J, K, M, N, R, S, T
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
TYK
Query on TYK

Download SDF File 
Download CCD File 
A
TYLOSIN
C46 H77 N O17
WBPYTXDJUQJLPQ-VMXQISHHSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
4, A, C, D, K, M, N, O, P, R, S, Z
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, 4, A, B, C, D, L, U, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
1, 2, 4, P, V
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 212.902α = 90.00
b = 300.474β = 90.00
c = 575.176γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance