4V5Q

The crystal structure of EF-Tu and G24A-tRNA-Trp bound to a near- cognate codon on the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.238

Literature

Macromolecules
Sequence Display for 4V5Q

Classification: RIBOSOME

Total Structure Weight: 4666721.00


Macromolecule Entities
Molecule Chains Length Organism Details
30S RIBOSOMAL PROTEIN S2 AB, CB 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S3 AC, CC 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S4 AD, CD 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S5 AE, CE 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S6 AF, CF 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S7 AG, CG 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S8 AH, CH 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S9 AI, CI 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S10 AJ, CJ 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S11 AK, CK 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S12 AL, CL 132 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S13 AM, CM 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S14 AN, CN 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S15 AO, CO 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S16 AP, CP 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S17 AQ, CQ 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S18 AR, CR 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S19 AS, CS 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S20 AT, CT 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN THX AU, CU 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ELONGATION FACTOR TU AZ, CZ 405 Thermus thermophilus Gene Name(s): tufA tuf TTHA1694
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L27 B0, D0 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L28 B1, D1 98 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 B2, D2 72 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 B3, D3 60 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L31 B4, D4 71 Thermus thermophilus Gene Name(s): rpmE TTHA1073
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L32 B5, D5 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L33 B6, D6 54 Thermus thermophilus Gene Name(s): rpmG rpl33 TTHA0250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L34 B7, D7 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L35 B8, D8 65 Thermus thermophilus Gene Name(s): rpmI TTHA0552
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L36 B9, D9 37 Thermus thermophilus Gene Name(s): rpmJ TTHA1668
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L1 BC, DC 229 Thermus thermophilus Gene Name(s): rplA TTHA0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L2 BD, DD 276 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 BE, DE 206 Thermus thermophilus Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 BF, DF 210 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 BG, DG 182 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 BH, DH 180 Thermus thermophilus Gene Name(s): rplF TTHA1677
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L10 BJ, DJ 173 Thermus thermophilus Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA
50S RIBOSOMAL PROTEIN L11 BK, DK 147 Thermus thermophilus Details: BUILT AS POLY-ALA
50S RIBOSOMAL PROTEIN L13 BN, DN 140 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 BO, DO 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 BP, DP 150 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 BQ, DQ 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L17 BR, DR 118 Thermus thermophilus Gene Name(s): rplQ rpl17 TTHA1663
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18 BS, DS 112 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 BT, DT 146 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L20 BU, DU 118 Thermus thermophilus Gene Name(s): rplT TTHA0553
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21 BV, DV 101 Thermus thermophilus Gene Name(s): rplU TTHA1783
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 BW, DW 113 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 BX, DX 96 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 BY, DY 110 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L25 BZ, DZ 206 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S RRNA AA, CA 1522 Thermus thermophilus CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AVY.
E-SITE TRNA PHE OR P-SITE TRNA PHE AV, AW, CV, CW 76 Escherichia coli
MRNA AX, CX 27 Escherichia coli
A-SITE TRNA G24A TRP-TRNA TRP AY, CY 77 Escherichia coli MUTATION AT G24A
23S RIBOSOMAL RNA BA, DA 2915 Thermus thermophilus CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
5S RIBOSOMAL RNA BB, DB 122 Thermus thermophilus

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

AZ, CZ KIRROMYCIN
MOCIMYCIN; DELVOMYCIN; MYC-8003 (Synonym)
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

AZ, CZ GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

AD, AN, B4, B9, CD, CN, D4, D9 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 8 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
BJ, BK, DJ, DK L-PEPTIDE LINKING C4 H9 N O2 --
4SU
Query on 4SU
AY, CY RNA LINKING C9 H13 N2 O8 P S U
H2U
Query on H2U
AY, CY RNA LINKING C9 H15 N2 O9 P U
OMC
Query on OMC
AY, CY RNA LINKING C10 H16 N3 O8 P C
MIA
Query on MIA
AY, CY RNA LINKING C16 H26 N5 O7 P S A
7MG
Query on 7MG
AY, CY RNA LINKING C11 H18 N5 O8 P G
5MU
Query on 5MU
AY, CY RNA LINKING C10 H15 N2 O9 P U
PSU
Query on PSU
AY, CY RNA LINKING C9 H13 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.238
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 289.90 α = 90.00
b = 269.40 β = 91.51
c = 404.50 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2010-12-07
  • Released Date: 2014-07-09
  • Deposition author(s): Schmeing, T.M., Voorhees, R.M., Ramakrishnan, V.
  • Previous versions: 2Y0Y 2Y0Z 2Y12 2Y13

Revision History

  • 2014-12-10
    Type: Other