3CD6

Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.

Blaha, G., Gurel, G., Schroeder, S.J., Moore, P.B., Steitz, T.A.

(2008) J Mol Biol 379: 505-519

  • DOI: 10.1016/j.jmb.2008.03.075
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Eleven mutations that make Haloarcula marismortui resistant to anisomycin, an antibiotic that competes with the amino acid side chains of aminoacyl tRNAs for binding to the A-site cleft of the large ribosomal unit, have been identified in 23S rRNA. T ...

    Eleven mutations that make Haloarcula marismortui resistant to anisomycin, an antibiotic that competes with the amino acid side chains of aminoacyl tRNAs for binding to the A-site cleft of the large ribosomal unit, have been identified in 23S rRNA. The correlation observed between the sensitivity of H. marismortui to anisomycin and the affinity of its large ribosomal subunits for the drug indicates that its response to anisomycin is determined primarily by the binding of the drug to its large ribosomal subunit. The structures of large ribosomal subunits containing resistance mutations show that these mutations can be divided into two classes: (1) those that interfere with specific drug-ribosome interactions and (2) those that stabilize the apo conformation of the A-site cleft of the ribosome relative to its drug-bound conformation. The conformational effects of some mutations of the second kind propagate through the ribosome for considerable distances and are reversed when A-site substrates bind to the ribosome.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2PA240Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P20276
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13PJ145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P29198
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14PK132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P22450
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15PL165Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12737
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15eM196Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P60618
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18PN187Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18eO116Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19eP149Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21eQ96Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22PR155Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23PS85Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12732
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3PB338Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24PT120Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P10972
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24eU67Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14116
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29PV71Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30PW154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31eX92Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32eY241Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AeZ116Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e157Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P32410
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e250Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P22452
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E392Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P32411
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4PC246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12735 
Go to UniProtKB:  P12735
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5PD177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14124
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6PE178Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14135 
Go to UniProtKB:  P14135
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AeF120Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12743 
Go to UniProtKB:  P12743
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10EG348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P15825 
Go to UniProtKB:  P15825
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10eH177Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60617 
Go to UniProtKB:  P60617
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11PI162Haloarcula marismortuiMutation(s): 0 
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14122 
Go to UniProtKB:  P14122
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  • Reference Sequence

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Entity ID: 30
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02923Haloarcula marismortui

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Entity ID: 31
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
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Entity ID: 32
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*(PPU))-3')43N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD
Download CCD File 
1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
SR
Query on SR
Download CCD File 
0, 1, 3, 9, A, B, F, J, R, S
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-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, R, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download CCD File 
0, 9, A, B, K, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download CCD File 
0, 9, B, C, H, J, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.805α = 90
b = 299.997β = 90
c = 576.002γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-02-26 
  • Released Date: 2008-05-20 
    • Deposition Author(s): Blaha, G., Gurel, G.

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2015-05-27
    Changes: Source and taxonomy
  • Version 1.3: 2017-10-25
    Changes: Refinement description