4XEJ

IRES bound to bacterial Ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.246

Literature

Macromolecules
Sequence Display for 4XEJ

Classification: RIBOSOME

Total Structure Weight: 4366159.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 AL02, BL02 271 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 AL03, BL03 204 Thermus thermophilus Gene Name(s): rplC TT_C1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 AL04, BL04 202 Thermus thermophilus Gene Name(s): rplD TT_C1327
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 AL05, BL05 181 Thermus thermophilus Gene Name(s): rplE TT_C1316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 AL06, BL06 159 Thermus thermophilus Gene Name(s): rplF TT_C1313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 AL09, BL09 145 Thermus thermophilus Gene Name(s): rplI TT_C1743
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 AL11, BL11 147 Thermus thermophilus Gene Name(s): rplK TT_C1738
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 AL13, BL13 137 Thermus thermophilus Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 AL14, BL14 122 Thermus thermophilus Gene Name(s): rplN TT_C1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 AL15, BL15 146 Thermus thermophilus Gene Name(s): rplO TT_C1309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 AL16, BL16 134 Thermus thermophilus Gene Name(s): rplP TT_C1321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 AL17, BL17 117 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 AL18, BL18 98 Thermus thermophilus Gene Name(s): rplR TT_C1312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 AL19, BL19 137 Thermus thermophilus Gene Name(s): rplS TT_C0669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 AL20, BL20 117 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 AL21, BL21 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 AL22, BL22 112 Thermus thermophilus Gene Name(s): rplV TT_C1323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 AL23, BL23 92 Thermus thermophilus Gene Name(s): rplW TT_C1326
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 AL24, BL24 100 Thermus thermophilus Gene Name(s): rplX TT_C1317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 AL25, BL25 187 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 AL27, BL27 76 Thermus thermophilus Gene Name(s): rpmA TT_C1423
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 AL28, BL28 88 Thermus thermophilus Gene Name(s): rpmB TT_C1964
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 AL29, BL29 62 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 AL30, BL30 59 Thermus thermophilus Gene Name(s): rpmD TT_C1310
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 AL32, BL32 52 Thermus thermophilus Gene Name(s): rpmF rpl32 TT_C0050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 AL33, BL33 44 Thermus thermophilus Gene Name(s): rpmG TT_C1735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 AL34, BL34 48 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 AL35, BL35 63 Thermus thermophilus Gene Name(s): rpmI TT_C0184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 AS02, BS02 234 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 AS03, BS03 206 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 AS04, BS04 208 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 AS05, BS05 151 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 AS06, BS06 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 AS07, BS07 155 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 AS08, BS08 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 AS09, BS09 127 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 AS10, BS10 98 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 AS11, BS11 114 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 AS12, BS12 122 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AS13, BS13 117 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 AS14, BS14 60 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 AS15, BS15 88 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 AS16, BS16 83 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 AS17, BS17 99 Thermus thermophilus Gene Name(s): rpsQ rps17 TT_C1319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AS18, BS18 70 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AS19, BS19 78 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 AS20, BS20 99 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx ATHX, BTHX 24 Thermus thermophilus Gene Name(s): rpsU TT_C1030
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 AL31, BL31 30 Thermus thermophilus Gene Name(s): rpmE TT_C0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A16S, B16S 1506 Thermus thermophilus
23S ribosomal RNA A23S, B23S 2879 Thermus thermophilus
5S ribosomal RNA A5S, B5S 119 Thermus thermophilus
IRES RNA AIRE, BIRE 196 Plautia stali intestine virus

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

AS04, AS14, BS04, BS14 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.246
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 209.05 α = 90.00
b = 447.22 β = 90.00
c = 608.96 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2014-12-23
  • Released Date: 2015-02-25
  • Deposition author(s): Zhu, J., Korostelev, A., Noller, H.F., Donohue, J.P.

Revision History

  • Version 1_0: 2015-02-25

    Type: Initial release

  • Version 1_1: 2015-03-18

    Type: Database references

  • Version 1_2: 2015-08-26

    Type: Data collection

  • Version 1_3: 2016-07-06

    Type: Data collection

  • Version 1_4: 2016-09-28

    Type: Data collection

  • Version 1_5: 2017-09-27

    Type: Author supporting evidence, Derived calculations, Structure summary