4WZD

Complex of 70S ribosome with cognate tRNA-Tyr in the P-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.227

Literature

Macromolecules
Sequence Display for 4WZD

Classification: RIBOSOME

Total Structure Weight: 4542795.50


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 12, 1E 256 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 22, 2E 239 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 32, 3E 209 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 42, 4E 162 Thermus thermophilus Gene Name(s): rpsE rps5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 52, 5E 101 Thermus thermophilus Gene Name(s): rpsF rps6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 62, 6E 156 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 72, 7E 138 Thermus thermophilus Gene Name(s): rpsH rps8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 82, 8E 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 1A, 1I 105 Thermus thermophilus Gene Name(s): rpsJ rps10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 2A, 2I 129 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 3A, 3I 132 Thermus thermophilus Gene Name(s): rpsL rps12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 4A, 4I 126 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z 5A, 5I 61 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 6A, 6I 89 Thermus thermophilus Gene Name(s): rpsO rps15
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 7A, 7I 88 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 8A, 8I 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 9A, 9I 88 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AA, AI 93 Thermus thermophilus Gene Name(s): rpsS rps19
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 BA, BI 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx 1B, 1F 27 Thermus thermophilus Gene Name(s): rpsU
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L1 71, 79 229 Thermus thermophilus Gene Name(s): rplA rpl1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 11, 19 276 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 21, 29 206 Thermus thermophilus Gene Name(s): rplC rpl3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 31, 39 210 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 41, 49 182 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 51, 59 180 Thermus thermophilus Gene Name(s): rplF rpl6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 61, 69 148 Thermus thermophilus Gene Name(s): rplI TTHA0242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 15, 58 140 Thermus thermophilus Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 25, 68 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 35, 78 150 Thermus thermophilus Gene Name(s): rplO rpl15
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 45, 88 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 55, 98 118 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 65, A8 112 Thermus thermophilus Gene Name(s): rplR rpl18
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 75, B8 146 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 85, C8 118 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 95, D8 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 A5, E8 113 Thermus thermophilus Gene Name(s): rplV rpl22
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 B5, F8 96 Thermus thermophilus Gene Name(s): rplW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 C5, G8 110 Thermus thermophilus Gene Name(s): rplX rpl24
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 D5, H8 206 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 E5, I8 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 F5, J8 98 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 G5, K8 72 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 H5, L8 60 Thermus thermophilus Gene Name(s): rpmD rpl30
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 I5, M8 71 Thermus thermophilus Gene Name(s): rpmE TT_C0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 J5, N8 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 K5, O8 54 Thermus thermophilus Gene Name(s): rpmG TT_C1735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 L5, P8 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 M5, Q8 65 Thermus thermophilus Gene Name(s): rpmI rpl35
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA 13, 1G 1522 Thermus thermophilus
tRNA-Tyr 2K, 2L, 3K, 3L 85 Escherichia coli
mRNA 4K, 4L 30 Thermus thermophilus
23S ribosomal RNA 14, 1H 2917 Thermus thermophilus
5S ribosomal RNA 16, 1J 122 Thermus thermophilus

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

32, 3E, 5A, 5I, C5, G8 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

11, 13, 14, 15, 16, 19, 1G, 1H, 1J, 21, 25, 29, 2A, 2K, 2L, 31, 32, 39, 3A, 3K, 3L, 42, 45, 4A, 4K, 52, 55, 5E, 7E, 88, 98, C5, E5, F5, G8, I8, Q8 MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 6 Unique
ID Chains Type Formula 2D Diagram Parent
4SU
Query on 4SU
2K, 2L, 3K, 3L RNA LINKING C9 H13 N2 O8 P S U
OMG
Query on OMG
2K, 2L, 3K, 3L RNA LINKING C11 H16 N5 O8 P G
QUO
Query on QUO
2K, 2L, 3K, 3L RNA LINKING C17 H26 N5 O10 P G
MIA
Query on MIA
2K, 2L, 3K, 3L RNA LINKING C16 H26 N5 O7 P S A
PSU
Query on PSU
2K, 2L, 3K, 3L RNA LINKING C9 H13 N2 O9 P U
5MU
Query on 5MU
2K, 2L, 3K, 3L RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.227

Unit Cell:

Length (Å) Angle (°)
a = 210.70 α = 90.00
b = 448.40 β = 90.00
c = 616.30 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2014-11-19
  • Released Date: 2015-06-10
  • Deposition author(s): Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

Revision History

  • Version 1_0: 2015-06-10

    Type: Initial release

  • Version 1_1: 2015-06-17

    Type: Database references

  • Version 1_2: 2016-01-27

    Type: Structure summary