4DR4

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound

• PDB DOI: https://doi.org/10.2210/pdb4DR4/pdb
• NAKB: 4DR4

• Classification: RIBOSOME/ANTIBIOTIC
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 2012-02-16 Released: 2012-11-14 
• Deposition Author(s): Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.97 Å
• R-Value Free: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

A structural basis for streptomycin-induced misreading of the genetic code.

Demirci, H., Murphy, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.

(2013) Nat Commun 4: 1355-1355

• PubMed: 23322043 
• DOI: https://doi.org/10.1038/ncomms2346
• Primary Citation of Related Structures:  
  4DR1, 4DR2, 4DR3, 4DR4, 4DR5, 4DR6, 4DR7


• PubMed Abstract: 
  

  During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.

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Organizational Affiliation: 

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 809.51 kDa 
• Atom Count: 53,651 
• Modelled Residue Count: 3,924 
• Deposited Residue Count: 4,081 
• Unique protein chains: 20
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L	135	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	N	61	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6  Go to UniProtKB:  P0DOY6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7  Go to UniProtKB:  P0DOY7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein THX	U	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*U)-3'	V	3	Thermus thermophilus HB8

Entity ID: 23
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'	W	15	Thermus thermophilus HB8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAR	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], X [auth A], Y [auth A], Z [auth A]	PAROMOMYCIN C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN	QN [auth D], ZN [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth A], AH [auth A], AI [auth A], AJ [auth A], AK [auth A], AL [auth A], AM [auth A], AN [auth A], AO [auth N], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth A], BH [auth A], BI [auth A], BJ [auth A], BK [auth A], BL [auth A], BM [auth A], BN [auth A], BO [auth O], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth A], CH [auth A], CI [auth A], CJ [auth A], CK [auth A], CL [auth A], CM [auth A], CN [auth A], CO [auth P], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth A], DH [auth A], DI [auth A], DJ [auth A], DK [auth A], DL [auth A], DM [auth A], DN [auth A], DO [auth P], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth A], EH [auth A], EI [auth A], EJ [auth A], EK [auth A], EL [auth A], EM [auth A], EN [auth A], EO [auth P], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], FG [auth A], FH [auth A], FI [auth A], FJ [auth A], FK [auth A], FL [auth A], FM [auth A], FN [auth A], FO [auth Q], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GG [auth A], GH [auth A], GI [auth A], GJ [auth A], GK [auth A], GL [auth A], GM [auth A], GN [auth A], GO [auth S], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth A], HH [auth A], HI [auth A], HJ [auth A], HK [auth A], HL [auth A], HM [auth A], HN [auth A], HO [auth S], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], IG [auth A], IH [auth A], II [auth A], IJ [auth A], IK [auth A], IL [auth A], IM [auth A], IN [auth A], IO [auth T], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth A], JH [auth A], JI [auth A], JJ [auth A], JK [auth A], JL [auth A], JM [auth A], JN [auth A], JO [auth V], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth A], KH [auth A], KI [auth A], KJ [auth A], KK [auth A], KL [auth A], KM [auth A], KN [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth A], LH [auth A], LI [auth A], LJ [auth A], LK [auth A], LL [auth A], LM [auth A], LN [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], MG [auth A], MH [auth A], MI [auth A], MJ [auth A], MK [auth A], ML [auth A], MM [auth A], MN [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], NG [auth A], NH [auth A], NI [auth A], NJ [auth A], NK [auth A], NL [auth A], NM [auth A], NN [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth A], OG [auth A], OH [auth A], OI [auth A], OJ [auth A], OK [auth A], OL [auth A], OM [auth A], ON [auth A], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth A], PI [auth A], PJ [auth A], PK [auth A], PL [auth A], PM [auth A], PN [auth A], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth A], QH [auth A], QI [auth A], QJ [auth A], QK [auth A], QL [auth A], QM [auth A], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RF [auth A], RG [auth A], RH [auth A], RI [auth A], RJ [auth A], RK [auth A], RL [auth A], RM [auth A], RN [auth D], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SF [auth A], SG [auth A], SH [auth A], SI [auth A], SJ [auth A], SK [auth A], SL [auth A], SM [auth A], SN [auth D], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], TF [auth A], TG [auth A], TH [auth A], TI [auth A], TJ [auth A], TK [auth A], TL [auth A], TM [auth A], TN [auth E], UA [auth A], UB [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth A], UG [auth A], UH [auth A], UI [auth A], UJ [auth A], UK [auth A], UL [auth A], UM [auth A], UN [auth E], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth A], VF [auth A], VG [auth A], VH [auth A], VI [auth A], VJ [auth A], VK [auth A], VL [auth A], VM [auth A], VN [auth E], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth A], WG [auth A], WH [auth A], WI [auth A], WJ [auth A], WK [auth A], WL [auth A], WM [auth A], WN [auth E], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XF [auth A], XG [auth A], XH [auth A], XI [auth A], XJ [auth A], XK [auth A], XL [auth A], XM [auth A], XN [auth H], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], YH [auth A], YI [auth A], YJ [auth A], YK [auth A], YL [auth A], YM [auth A], YN [auth L], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZF [auth A], ZG [auth A], ZH [auth A], ZI [auth A], ZJ [auth A], ZK [auth A], ZL [auth A], ZM [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0TD	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.97 Å
• R-Value Free:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 400.951	α = 90
b = 400.951	β = 90
c = 176.675	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2013-01-30
  Changes: Database references
• Version 1.3: 2025-02-19
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary