1TTT | pdb_00001ttt

Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex

PDB DOI: https://doi.org/10.2210/pdb1TTT/pdb
NAKB: 1TTT

Classification: COMPLEX (ELONGATION FACTOR/TRNA)
Organism(s): Thermus aquaticus
Mutation(s): No

Deposited: 1995-11-16 Released: 1996-12-23
Deposition Author(s): Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F.C., Nyborg, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.290 (Depositor)
R-Value Work:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.

Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F., Nyborg, J.

(1995) Science 270: 1464-1472

PubMed: 7491491 Search on PubMed
DOI: https://doi.org/10.1126/science.270.5241.1464
Primary Citation Related Structures:
1TTT

PubMed Abstract:
The structure of the ternary complex consisting of yeast phenylalanyl-transfer RNA (Phe-tRNAPhe), Thermus aquaticus elongation factor Tu (EF-Tu), and the guanosine triphosphate (GTP) analog GDPNP was determined by x-ray crystallography at 2.7 angstrom resolution. The ternary complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome. The EF-Tu-GDPNP component binds to one side of the acceptor helix of Phe-tRNAPhe involving all three domains of EF-Tu. Binding sites for the phenylalanylated CCA end and the phosphorylated 5' end are located at domain interfaces, whereas the T stem interacts with the surface of the beta-barrel domain 3. The binding involves many conserved residues in EF-Tu. The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus.

Organizational Affiliation

Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark.

Macromolecule Content

Total Structure Weight: 211.11 kDa
Atom Count: 14,573
Modeled Residue Count: 1,443
Deposited Residue Count: 1,443
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
OF ELONGATION FACTOR TU (EF-TU)	D [auth A], E [auth B], F [auth C]	405	Thermus aquaticus	Mutation(s): 0 EC: 3.6.5.3
UniProt
Find proteins for Q01698 (Thermus aquaticus) Explore Q01698 Go to UniProtKB: Q01698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01698
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
TRANSFER RIBONUCLEIC ACID (YEAST, PHE)	A [auth D], B [auth E], C [auth F]	76	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A]	N [auth A], P [auth B], R [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C]
PHE Query on PHE Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain J [auth E] SDF format, chain H [auth D] MOL2 format, chain L [auth F] MOL2 format, chain J [auth E] MOL2 format, chain H [auth D] mmCIF format, chain L [auth F] mmCIF format, chain J [auth E] mmCIF format, chain H [auth D]	H [auth D], J [auth E], L [auth F]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain H [auth D] Focus chain J [auth E] Focus chain L [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain K [auth F] SDF format, chain I [auth E] SDF format, chain G [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth F] MOL2 format, chain I [auth E] MOL2 format, chain G [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth F] mmCIF format, chain I [auth E] mmCIF format, chain G [auth D]	G [auth D] I [auth E] K [auth F] M [auth A] O [auth B] G [auth D], I [auth E], K [auth F], M [auth A], O [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain I [auth E] Focus chain K [auth F] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.290 (Depositor)
R-Value Work: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 206.835	α = 90
b = 122.354	β = 126.3
c = 151.552	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
DENZO	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 1996-12-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1996-12-23
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Other