4V6F

Elongation complex of the 70S ribosome with three tRNAs and mRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.215

Literature

Macromolecules
Sequence Display for 4V6F

Classification: RIBOSOME

Total Structure Weight: 4678981.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L2 AD, DD 276 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 AE, DE 206 Thermus thermophilus Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 AF, DF 210 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 AG, DG 182 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 AH, DH 180 Thermus thermophilus Gene Name(s): rplF TTHA1677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L9 AK, DK 148 Thermus thermophilus Gene Name(s): rplI TTHA0242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L13 AM, DM 140 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 AN, DN 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 AO, DO 150 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 AP, DP 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L17 A0, D0 118 Thermus thermophilus Gene Name(s): rplQ rpl17 TTHA1663
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18 AQ, DQ 112 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 AR, DR 146 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L20 A1, D1 118 Thermus thermophilus Gene Name(s): rplT TTHA0553
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21 A2, D2 101 Thermus thermophilus Gene Name(s): rplU TTHA1783
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 AS, DS 113 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 AT, DT 96 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 AU, DU 110 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L25 AV, DV 206 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L27 A3, D3 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L28 AZ, DZ 98 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 AW, DW 72 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 AX, DX 60 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L31 A4, D4 71 Thermus thermophilus Gene Name(s): rpmE TTHA1073
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L32 A5, D5 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L33 A6, D6 54 Thermus thermophilus Gene Name(s): rpmG rpl33 TTHA0250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L34 A7, D7 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L35 A8, D8 65 Thermus thermophilus Gene Name(s): rpmI TTHA0552
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 BE, CE 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 BF, CF 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 BG, CG 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 BH, CH 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 BI, CI 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 BJ, CJ 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 BK, CK 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 BL, CL 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 BM, CM 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 BN, CN 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 BO, CO 132 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 BP, CP 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z BQ, CQ 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 BR, CR 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 BS, CS 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 BT, CT 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 BU, CU 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 BV, CV 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 BW, CW 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx BX, CX 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7/L12 DI, DJ 125 Thermus thermophilus Gene Name(s): rplL TTHA0210
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10 DY 173 Thermus thermophilus Gene Name(s): rplJ TTHA0209
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 DL 147 Thermus thermophilus Gene Name(s): rplK TTHA0247
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA AA 2909 Thermus thermophilus
5S RIBOSOMAL RNA AB, DB 122 Thermus thermophilus
16S ribosomal RNA BA 1516 Thermus thermophilus
TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37 BB, BC, BD... , CB, CC, CD BB, BC, BD, CB, CC, CD 76 Escherichia coli
MRNA B1, C1 30 synthetic
16S ribosomal RNA CA 1515 Thermus thermophilus
23S RRNA DA 2912 Thermus thermophilus

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

A4, BG, BQ, CG, CQ, D4 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A0, A1, A2, A3, A5, A6, A7, A8, AA, AB, AD, AE, AF, AG, AH, AK, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AZ, B1, BA, BB, BC, BD, BE, BF, BG, BH, BI, BK, BL, BM, BO, BP, BQ, BS, BT, BU, BV, BW, BX, C1, CA, CB, CC, CD, CE, CF, CG, CH, CI, CJ, CK, CL, CM, CN, CP, CQ, CR, CS, CT, CV, CW, D0, D1, D2, D3, D4, D5, D6, D7, D8, DA, DB, DD, DE, DF, DG, DH, DK, DL, DM, DN, DO, DP, DQ, DR, DS, DT, DU, DV, DW, DX, DY, DZ MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MIA
Query on MIA
BB, BC, BD, CB, CC, CD RNA LINKING C16 H26 N5 O7 P S A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.215
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 209.46 α = 90.00
b = 446.20 β = 90.00
c = 623.05 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2009-07-09
  • Released Date: 2014-07-09
  • Deposition author(s): Jenner, L.B., Yusupova, G., Yusupov, M.
  • Previous versions: 3I8F 3I8G 3I8H 3I8I

Revision History

  • 2014-12-10
    Type: Other
  • 2017-05-31
    Type: Other