Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZab 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1366820.63 
• Atom Count: 84444 
• Residue Count: 6575 
• Unique protein chains: 29
• Unique nucleic acid chains: 2

2ZJP

Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans

• DOI: 10.2210/pdb2ZJP/pdb
• NDB: RR0215

• Classification: RIBOSOME/ANTIBIOTIC
• Organism(s): Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422), Deinococcus radiodurans, Streptomyces actuosus


• Deposited: 2008-03-07 Released: 2008-06-17 
• Deposition Author(s): Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M.T., Fucini, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.7 Å
• R-Value Free: 0.340 
• R-Value Work: 0.300 

Literature

Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin.

Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M., Fucini, P.

(2008) Mol.Cell 30: 26

• PubMed: 18406324 
• DOI: 10.1016/j.molcel.2008.01.009
• Primary Citation of Related Structures:  
  3CF5, 2ZJR, 2ZJQ


• PubMed Abstract: 
  

The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis.

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Organizational Affiliation: 

Cluster of Excellence for Macromolecular Complexes, Institut für Organische Chemie und Chemische Biologie, J.W. Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L33	1	55	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmG
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L34	2	47	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmH
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSH2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L35	3	66	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmI
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSW6

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L36	4	37	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmJ
Find proteins for Q9RSK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSK0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
NOSIHEPTIDE	5	13	Streptomyces actuosus	Mutation(s): 0  Gene Names: nosM
Find proteins for C6FX52 (Streptomyces actuosus) Go to UniProtKB:  C6FX52

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L2	A	274	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplB
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ9

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L3	B	211	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplC
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXK2

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L4	C	205	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplD
Find proteins for Q9RXK1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXK1

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L5	D	180	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplE
Find proteins for Q9RXJ0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L6	E	185	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplF
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSL3

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L11	F	144	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplK
Find proteins for Q9RSS7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSS7

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L13	G	174	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplM
Find proteins for Q9RXY1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXY1

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L14	H	134	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplN
Find proteins for Q9RXJ2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ2

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L15	I	156	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplO
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSK9

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L16	J	142	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplP
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L17	K	116	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplQ
Find proteins for Q9RSJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSJ5

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L18	L	114	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplR
Find proteins for Q9RSL2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSL2

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L19	M	166	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplS
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RWB4

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L20	N	118	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplT
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSW7

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L21	O	100	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplU
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RY64

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L22	P	134	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplV
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ7

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L23	Q	95	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplW
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXK0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L24	R	115	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplX
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ1

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L25	S	237	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplY (ctc)
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RX88

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L27	T	91	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmA
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RY65

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L28	U	81	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmB
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RRG8

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L29	V	67	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmC
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RXJ4

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L30	W	55	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmD
Find proteins for Q9RSL0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RSL0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L32	Y	60	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rpmF
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  P49228

Entity ID: 29
Molecule	Chains	Length	Organism
RIBOSOMAL 23S RNA	X	2880	Deinococcus radiodurans

Entity ID: 31
Molecule	Chains	Length	Organism
RIBOSOMAL 5S RNA	Z	123	Deinococcus radiodurans

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	4, Y	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	M, X, Z	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NO1	5	4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid C11 H11 N O3 BSECKLZXEJBFRE-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000221	5	Nosiheptide	Thiopeptide / Antibiotic		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.7 Å
• R-Value Free: 0.340 
• R-Value Work: 0.300 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 169.900	α = 90.00
b = 408.900	β = 90.00
c = 694.500	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-07 
• Released Date: 2008-06-17 
• Deposition Author(s): Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M.T., Fucini, P.

Revision History 

• Version 1.0: 2008-06-17
  Type: Initial release
• Version 1.1: 2011-06-14
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-07-27
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2011-11-30
  Type: Database references
• Version 1.5: 2011-12-28
  Type: Atomic model, Derived calculations
• Version 1.6: 2012-12-12
  Type: Other