4V4J

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.351
  • R-Value Work: 0.327

Literature

Macromolecules
Sequence Display for 4V4J

Classification: RIBOSOME

Total Structure Weight: 2224546.50


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L1 A 229 Thermus thermophilus Gene Name(s): rplA TT_C1739
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 B 276 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 C 206 Thermus thermophilus Gene Name(s): rplC TT_C1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 D 205 Thermus thermophilus Gene Name(s): rplD TT_C1327
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 E 182 Thermus thermophilus Gene Name(s): rplE TT_C1316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 F 180 Thermus thermophilus Gene Name(s): rplF TT_C1313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 G 148 Thermus thermophilus Gene Name(s): rplI TT_C1743
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 H 140 Thermus thermophilus Mutation: M24V
Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 I 122 Thermus thermophilus Gene Name(s): rplN TT_C1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 J 150 Thermus thermophilus Gene Name(s): rplO TT_C1309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 K 141 Thermus thermophilus Gene Name(s): rplP TT_C1321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 L 118 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 M 112 Thermus thermophilus Gene Name(s): rplR TT_C1312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 N 146 Thermus thermophilus Gene Name(s): rplS TT_C0669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 O 118 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 P 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 Q 113 Thermus thermophilus Gene Name(s): rplV TT_C1323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 R 96 Thermus thermophilus Gene Name(s): rplW TT_C1326
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 S 110 Thermus thermophilus Gene Name(s): rplX TT_C1317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 T 206 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 U 85 Thermus thermophilus Gene Name(s): rpmA TT_C1423
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LSU ribosomal protein L28P V 98 Thermus thermophilus Gene Name(s): rpmB TT_C1964
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 W 72 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LSU ribosomal protein L30P X 60 Thermus thermophilus Gene Name(s): rpmD TT_C1310
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 Y 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TT_C0050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 Z 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 a 65 Thermus thermophilus Gene Name(s): rpmI TT_C0184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 b 37 Thermus thermophilus Gene Name(s): rpmJ TT_C1304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 c 256 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 d 239 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 e 209 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 f 162 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 g 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 h 156 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 i 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 j 128 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 k 105 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 l 129 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 m 132 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 n 126 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z o 61 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 p 89 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 q 88 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 r 105 Thermus thermophilus Gene Name(s): rpsQ rps17 TT_C1319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 s 88 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 t 93 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 u 106 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx v 27 Thermus thermophilus Gene Name(s): rpsU TT_C1030
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S LARGE SUBUNIT RIBOSOMAL RNA w 2889 Thermus thermophilus
5S LARGE SUBUNIT RIBOSOMAL RNA x 120 Thermus thermophilus
16S RNA y 1522 Thermus thermophilus
P-site tRNAfMET z 77 Thermus thermophilus
E-site tRNA 2 76 Thermus thermophilus
MRNA 3 18 Thermus thermophilus

Small Molecules
Modified Residues 6 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
2, y RNA LINKING C9 H13 N2 O9 P U
7MG
Query on 7MG
y RNA LINKING C11 H18 N5 O8 P G
M2G
Query on M2G
y RNA LINKING C12 H18 N5 O8 P G
5MC
Query on 5MC
y RNA LINKING C10 H16 N3 O8 P C
2MG
Query on 2MG
y RNA LINKING C11 H16 N5 O8 P G
MA6
Query on MA6
y RNA LINKING C12 H18 N5 O7 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.83 Å
  • R-Value Free: 0.351
  • R-Value Work: 0.327
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 507.21 α = 90.00
b = 507.21 β = 90.00
c = 692.51 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2007-07-18
  • Released Date: 2014-07-09
  • Deposition author(s): Korostelev, A., Trakhanov, S., Asahara, H., Laurberg, M., Noller, H.F.
  • Previous versions: 1VSP 2QNH

Revision History

  • 2014-12-10
    Type: Other