4V42

Crystal structure of the ribosome at 5.5 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Work:

Literature

Macromolecules
Sequence Display for 4V42

Classification: RIBOSOME

Total Structure Weight: 2203915.25


Macromolecule Entities
Molecule Chains Length Organism Details
30S RIBOSOMAL PROTEIN S2 AE 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S3 AF 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S4 AG 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S5 AH 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S6 AI 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S7 AJ 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S8 AK 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S9 AL 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S10 AM 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S11 AN 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S12 AO 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S13 AP 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S14 AQ 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S15 AR 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S16 AS 91 Thermus thermophilus
30S RIBOSOMAL PROTEIN S17 AT 105 Thermus thermophilus
30S RIBOSOMAL PROTEIN S18 AU 88 Thermus thermophilus
30S RIBOSOMAL PROTEIN S19 AV 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S20 AW 106 Thermus thermophilus
30S RIBOSOMAL PROTEIN THX AX 26 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L1 BC 228 Thermus thermophilus Gene Name(s): rplA TTHA0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L2 BD 178 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 BE 338 Thermus thermophilus Mutation: D113S, V114D, P115R, E116L, D119A, P120L, A122I, A123V, E125D
Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 BF 246 Thermus thermophilus Mutation: Q2E
Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 BG 176 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 BH 177 Thermus thermophilus Gene Name(s): rplF BVI061214_01035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L7/L12 BI, BJ 128 Thermus thermophilus Gene Name(s): rplL TTHA0210
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L9 BK 149 Thermus thermophilus Gene Name(s): rplI TTHA0242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L11 BL 141 Thermus thermophilus Gene Name(s): rplK TTHA0247
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L13 BM 145 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 BN 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 BO 164 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 BP 138 Thermus thermophilus
50S RIBOSOMAL PROTEIN L18 BQ 186 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 BR 66 Thermus thermophilus Gene Name(s): rpl24e rrnAC0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 BS 113 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 BT 84 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 BU 119 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L25 BV 94 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 BW 70 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 BX 60 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
30S 16S RIBOSOMAL RNA AA 1522 Thermus thermophilus
TRNA(PHE) AB, AC 76 synthetic A-SITE TRNA CHAIN B, P-SITE TRNA CHAIN C
TRNA(PHE) AD 74 synthetic E-SITE TRNA
A- AND P-SITE MESSENGER RNA CODONS A1 6 synthetic 6 NT LONG MRNA FRAGMENT
50S 23S RIBOSOMAL RNA BA 2916 Thermus thermophilus
50S 5S RIBOSOMAL RNA BB 123 Thermus thermophilus

Small Molecules
Modified Residues 12 Unique
ID Chains Type Formula 2D Diagram Parent
2MG
Query on 2MG
AB, AC RNA LINKING C11 H16 N5 O8 P G
H2U
Query on H2U
AB, AC, AD RNA LINKING C9 H15 N2 O9 P U
M2G
Query on M2G
AB, AC RNA LINKING C12 H18 N5 O8 P G
OMC
Query on OMC
AB, AC RNA LINKING C10 H16 N3 O8 P C
OMG
Query on OMG
AB, AC RNA LINKING C11 H16 N5 O8 P G
YG
Query on YG
AB, AC RNA LINKING C21 H29 N6 O12 P G
PSU
Query on PSU
AB, AC, AD RNA LINKING C9 H13 N2 O9 P U
5MC
Query on 5MC
AB, AC, AD RNA LINKING C10 H16 N3 O8 P C
7MG
Query on 7MG
AB, AC RNA LINKING C11 H18 N5 O8 P G
5MU
Query on 5MU
AB, AC, AD RNA LINKING C10 H15 N2 O9 P U
1MA
Query on 1MA
AB, AC RNA LINKING C11 H16 N5 O7 P A
4SU
Query on 4SU
AD RNA LINKING C9 H13 N2 O8 P S U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Observed:
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 507.20 α = 90.00
b = 507.20 β = 90.00
c = 803.66 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2001-03-30
  • Released Date: 2014-07-09
  • Deposition author(s): Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H.D., Noller, H.F.
  • This entry supercedes: 1GIX 1GIY

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other