4PC1 | pdb_00004pc1

Elongation Factor Tu:Ts complex with a bound phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4PC1

This is version 1.3 of the entry. See complete history

Literature

Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.

Thirup, S.S.Van, L.B.Nielsen, T.K.Knudsen, C.R.

(2015) J Struct Biol 191: 10-21

  • DOI: https://doi.org/10.1016/j.jsb.2015.06.011
  • Primary Citation Related Structures: 
    4PC1, 4PC2, 4PC3, 4PC6, 4PC7

  • PubMed Abstract: 

    Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.


  • Organizational Affiliation
    • Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark. Electronic address: sth@mbg.au.dk.

Macromolecule Content 

  • Total Structure Weight: 148.35 kDa 
  • Atom Count: 11,325 
  • Modeled Residue Count: 1,284 
  • Deposited Residue Count: 1,352 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor Tu
A, B
394Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: tufAtufECDH10B_3514
EC: 3.6.5.3
UniProt
Find proteins for A0A0M3KKV1 (Escherichia coli (strain K12 / DH10B))
Explore A0A0M3KKV1 
Go to UniProtKB:  A0A0M3KKV1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKV1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor Ts
C, D
282Escherichia coliMutation(s): 0 
Gene Names: tsfBN17_45931ECs0172LF82_2325
UniProt
Find proteins for C3TPM7 (Escherichia coli)
Explore C3TPM7 
Go to UniProtKB:  C3TPM7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3TPM7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PB

Query on PB



Download:Ideal Coordinates CCD File
H [auth C],
I [auth C]
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
K [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
J [auth C],
L [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.51α = 90
b = 109.77β = 90
c = 195.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2015-05-06 
  • Deposition Author(s): Thirup, S.S.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy