4V9N

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.234

Literature

Macromolecules
Sequence Display for 4V9N

Classification: RIBOSOME

Total Structure Weight: 4435849.50


Macromolecule Entities
Molecule Chains Length Organism Details
Bacterial peptide chain release factor 2 (RF-2) AY, CY 362 Thermus thermophilus Mutation: Q253P
Gene Name(s): TT_C1852
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 AB, CB 234 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 AC, CC 206 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 AD, CD 208 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 AE, CE 151 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 AF, CF 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 AG, CG 155 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 AH, CH 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 AI, CI 127 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 AJ, CJ 98 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 AK, CK 114 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 AL, CL 122 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AM, CM 117 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 AN, CN 60 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 AO, CO 88 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 AP, CP 83 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 AQ, CQ 99 Thermus thermophilus Gene Name(s): rpsQ rps17 TT_C1319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AR, CR 70 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AS, CS 78 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 AT, CT 99 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx AU, CU 24 Thermus thermophilus Gene Name(s): rpsU TT_C1030
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 BD, DD 271 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 BE, DE 204 Thermus thermophilus Gene Name(s): rplC TT_C1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 BF, DF 202 Thermus thermophilus Gene Name(s): rplD TT_C1327
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 BG, DG 181 Thermus thermophilus Gene Name(s): rplE TT_C1316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 BH, DH 159 Thermus thermophilus Gene Name(s): rplF TT_C1313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 BI, DI 145 Thermus thermophilus Gene Name(s): rplI TT_C1743
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 BK, DK 147 Thermus thermophilus Gene Name(s): rplK TT_C1738
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 BN, DN 137 Thermus thermophilus Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 BO, DO 122 Thermus thermophilus Gene Name(s): rplN TT_C1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 BP, DP 146 Thermus thermophilus Gene Name(s): rplO TT_C1309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 BQ, DQ 134 Thermus thermophilus Gene Name(s): rplP TT_C1321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 BR, DR 117 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 BS, DS 98 Thermus thermophilus Gene Name(s): rplR TT_C1312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 BT, DT 137 Thermus thermophilus Gene Name(s): rplS TT_C0669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 BU, DU 117 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 BV, DV 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 BW, DW 112 Thermus thermophilus Gene Name(s): rplV TT_C1323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 BX, DX 92 Thermus thermophilus Gene Name(s): rplW TT_C1326
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 BY, DY 100 Thermus thermophilus Gene Name(s): rplX TT_C1317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 BZ, DZ 187 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 B0, D0 76 Thermus thermophilus Gene Name(s): rpmA TT_C1423
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 B1, D1 88 Thermus thermophilus Gene Name(s): rpmB TT_C1964
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 B2, D2 62 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 B3, D3 59 Thermus thermophilus Gene Name(s): rpmD TT_C1310
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 B4, D4 30 Thermus thermophilus Gene Name(s): rpmE TT_C0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 B5, D5 52 Thermus thermophilus Gene Name(s): rpmF rpl32 TT_C0050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 B6, D6 44 Thermus thermophilus Gene Name(s): rpmG TT_C1735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 B7, D7 48 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 B8, D8 63 Thermus thermophilus Gene Name(s): rpmI TT_C0184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA (1504-MER) AA, CA 1504 Thermus thermophilus
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') AV, CV 10 Thermus thermophilus
P-site tRNA-fMet AW, CW 77 Thermus thermophilus
23S ribosomal RNA BA, DA 2879 Thermus thermophilus
5S ribosomal RNA BB, DB 119 Thermus thermophilus

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

AD, AN, CD, CN ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

AA, AC, AG, AO, AQ, AT, AV, AW, AY, B0, B1, B3, B5, B8, BA, BB, BD, BE, BF, BP, BT, BX, BY, CA, CD, CM, CR, CV, CW, CY, D0, D1, D5, D7, DA, DB, DD, DE, DF, DH, DI, DN, DP, DQ, DV, DW, DX MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.234
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 212.07 α = 90.00
b = 454.40 β = 90.00
c = 618.45 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2013-04-26
  • Released Date: 2014-07-09
  • Deposition author(s): Santos, N., Zhu, J., Donohue, J.P., Korostelev, A.A., Noller, H.F.
  • Previous versions: 4KFH 4KFI 4KFK 4KFL

Revision History

  • 2014-12-10
    Type: Other