5J4D

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 5J4D

Classification: RIBOSOME

Total Structure Weight: 4575464.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 E, JB 275 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 F, KB 206 Thermus thermophilus Gene Name(s): rplC TT_C1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 G, LB 205 Thermus thermophilus Gene Name(s): rplD TT_C1327
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 H, MB 182 Thermus thermophilus Gene Name(s): rplE TT_C1316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 I, NB 180 Thermus thermophilus Gene Name(s): rplF TT_C1313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 J, OB 148 Thermus thermophilus Gene Name(s): rplI TT_C1743
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 K, PB 140 Thermus thermophilus Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 L, QB 122 Thermus thermophilus Gene Name(s): rplN TT_C1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 M, RB 150 Thermus thermophilus Gene Name(s): rplO TT_C1309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 N, SB 141 Thermus thermophilus Gene Name(s): rplP TT_C1321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 O, TB 118 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 P, UB 112 Thermus thermophilus Gene Name(s): rplR TT_C1312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 Q, VB 146 Thermus thermophilus Gene Name(s): rplS TT_C0669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 R, WB 118 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 S, XB 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 T, YB 113 Thermus thermophilus Gene Name(s): rplV TT_C1323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 U, ZB 96 Thermus thermophilus Gene Name(s): rplW TT_C1326
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 AC, V 110 Thermus thermophilus Gene Name(s): rplX TT_C1317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 BC, W 206 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 CC, X 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 DC, Y 98 Thermus thermophilus Gene Name(s): rpmB TT_C1964
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 EC, Z 72 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 AA, FC 60 Thermus thermophilus Gene Name(s): rpmD TT_C1310
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 BA, GC 71 Thermus thermophilus Gene Name(s): rpmE TT_C0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 CA, HC 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TT_C0050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 DA, IC 54 Thermus thermophilus Gene Name(s): rpmG TT_C1735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 EA, JC 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 FA, KC 65 Thermus thermophilus Gene Name(s): rpmI TT_C0184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 GA, LC 37 Thermus thermophilus Gene Name(s): rpmJ TT_C1304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peptide chain release factor 1 JA, OC 368 Escherichia coli Gene Name(s): prfA sueB uar b1211 JW1202
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 KA, PC 256 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 LA, QC 239 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 MA, RC 209 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 NA, SC 162 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 OA, TC 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 PA, UC 156 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 QA, VC 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 RA, WC 128 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 SA, XC 105 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 TA, YC 129 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 UA, ZC 132 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AD, VA 126 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z BD, WA 61 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 CD, XA 89 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 DD, YA 88 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 ED, ZA 105 Thermus thermophilus Gene Name(s): rpsQ rps17 TT_C1319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AB, FD 88 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 BB, GD 93 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 CB, HD 106 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx DB, ID 27 Thermus thermophilus Gene Name(s): rpsU TT_C1030
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A, FB 1507 Thermus thermophilus
25S ribosomal RNA B, GB 2880 Thermus thermophilus
5S ribosomal RNA C, HB 120 Thermus thermophilus
tRNA D, IA, IB, NC 77 Escherichia coli
mRNA HA, MC 27 Synthetic construct

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

AC, BA, CA, DA, GA, GC, HC, IC, LC, V ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, AA, AD, B, BA, BB, BC, C, CA, CB, CC, CD, D, DA, DB, DC, DD, E, EA, EC, ED, F, FA, FB, FC, G, GA, GB, GC, GD, H, HA, HB, HC, HD, I, IA, IB, J, JA, JB, K, KA, KB, KC, L, LA, LB, M, MA, MB, MC, N, NA, NB, NC, O, OA, OB, OC, P, PA, PB, PC, Q, QA, QB, QC, R, RA, RB, RC, S, SA, SB, SC, T, TA, TB, TC, U, UA, UB, UC, VA, VB, VC, W, WA, WB, WC, X, XA, XB, XC, Y, YA, YB, YC, Z, ZA, ZB, ZC MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 14 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A, B, D, FB, GB, HA, IA, IB, MC, NC RNA LINKING C9 H13 N2 O9 P U
7MG
Query on 7MG
A, FB RNA LINKING C11 H18 N5 O8 P G
M2G
Query on M2G
A, FB RNA LINKING C12 H18 N5 O8 P G
5MC
Query on 5MC
A, B, D, FB, GB, IA, IB, NC RNA LINKING C10 H16 N3 O8 P C
2MG
Query on 2MG
A, FB RNA LINKING C11 H16 N5 O8 P G
4OC
Query on 4OC
A, B, FB, GB RNA LINKING C11 H18 N3 O8 P C
UR3
Query on UR3
A, FB RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
A, FB RNA LINKING C12 H18 N5 O7 P A
5MU
Query on 5MU
B, D, GB, IA, IB, NC RNA LINKING C10 H15 N2 O9 P U
OMG
Query on OMG
B, GB RNA LINKING C11 H16 N5 O8 P G
2MA
Query on 2MA
B, GB RNA LINKING C11 H16 N5 O7 P A
2MU
Query on 2MU
B, GB RNA LINKING C11 H17 N2 O9 P U
4SU
Query on 4SU
D, IA, IB, NC RNA LINKING C9 H13 N2 O8 P S U
0TD
Query on 0TD
UA, ZC L-PEPTIDE LINKING C5 H9 N O4 S ASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 211.54 α = 90.00
b = 454.40 β = 90.00
c = 619.47 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-03-31
  • Released Date: 2016-05-18
  • Deposition author(s): Svidritskiy, E., Korostelev, A.A.

Revision History

  • Version 1_0: 2016-05-18

    Type: Initial release

  • Version 1_1: 2016-06-08

    Type: Database references

  • Version 1_2: 2017-09-06

    Type: Author supporting evidence, Database references, Derived calculations