3T1H

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin

Structural Biology Knowledgebase: 3T1H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3T1H

Classification: Ribosome / Antibiotic

Total Structure Weight: 790490.84


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
30S ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
30S ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S ribosomal protein S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
30S ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
30S ribosomal protein S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
30S ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
30S ribosomal protein S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
30S ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
30S ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
30S ribosomal protein S12 L 132 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S ribosomal protein S14 type Z N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
30S ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S ribosomal protein S17 Q 105 Thermus thermophilus Gene Name(s): rpsQ rps17
30S ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR rps18
30S ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
30S ribosomal protein Thx V 27 Thermus thermophilus Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16s rRNA A 1513 Thermus thermophilus
mRNA A-site fragment W 3 synthetic
tRNA ASL human Lys3 X 11 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

A, B, L, S MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PAR
Query on PAR

A PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E (Synonym)
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
70U
Query on 70U
X RNA LINKING C12 H17 N2 O10 P S U
12A
Query on 12A
X RNA LINKING C16 H23 N6 O11 P S A
PSU
Query on PSU
X RNA LINKING C9 H13 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.247
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 402.30 α = 90.00
b = 402.30 β = 90.00
c = 175.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-07-21
  • Released Date: 2012-01-25
  • Deposition author(s): Murphy, F.V., Vendeix, F.A.P., Cantara, W., Leszczynska, G., Gustilo, E.M., Sproat, B., Malkiewicz, A.A.P., Agris, P.F.

Revision History

  • 2012-03-07
    Type: Citation | Details: Citation update