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- PDB-1ttt: Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex -

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Basic information

Entry
Database: PDB / ID: 1ttt
TitlePhe-tRNA, elongation factoR EF-TU:GDPNP ternary complex
Components
  • OF ELONGATION FACTOR TU (EF-TU)
  • TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
KeywordsCOMPLEX (ELONGATION FACTOR/TRNA) / PROTEIN SYNTHESIS / EF-TU / TRNA / RIBOSOME / 1EFT / 4TNA / PEPTIDE ELONGATION RIBONUCLEOPROTEIN / COMPLEX (ELONGATION FACTOR-TRNA) / COMPLEX (ELONGATION FACTOR-TRNA) complex
Function / homology
Function and homology information


protein-synthesizing GTPase / translation elongation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHENYLALANINE / RNA / RNA (> 10) / Elongation factor Tu
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsNissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J.
Citation
Journal: Science / Year: 1995
Title: Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F. / Nyborg, J.
#1: Journal: FEBS Lett. / Year: 1994
Title: Purification and Crystallization of the Ternary Complex of Elongation Factor TU:GTP and Phe-tRNA(Phe)
Authors: Nissen, P. / Reshetnikova, L. / Siboska, G. / Polekhina, G. / Thirup, S. / Kjeldgaard, M. / Clark, B.F. / Nyborg, J.
#2: Journal: Structure / Year: 1993
Title: The Crystal Structure of Elongation Factor EF-TU from Thermus Aquaticus in the GTP Conformation
Authors: Kjeldgaard, M. / Nissen, P. / Thirup, S. / Nyborg, J.
History
DepositionNov 16, 1995Processing site: NDB
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
E: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
F: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
A: OF ELONGATION FACTOR TU (EF-TU)
B: OF ELONGATION FACTOR TU (EF-TU)
C: OF ELONGATION FACTOR TU (EF-TU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,10718
Polymers208,8996
Non-polymers2,20812
Water90150
1
D: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
A: OF ELONGATION FACTOR TU (EF-TU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3696
Polymers69,6332
Non-polymers7364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-27.2 kcal/mol
Surface area26150 Å2
MethodPISA
2
E: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
B: OF ELONGATION FACTOR TU (EF-TU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3696
Polymers69,6332
Non-polymers7364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-30.2 kcal/mol
Surface area25990 Å2
MethodPISA
3
F: TRANSFER RIBONUCLEIC ACID (YEAST, PHE)
C: OF ELONGATION FACTOR TU (EF-TU)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3696
Polymers69,6332
Non-polymers7364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-25.4 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.835, 122.354, 151.552
Angle α, β, γ (deg.)90.00, 126.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain / Protein , 2 types, 6 molecules DEFABC

#1: RNA chain TRANSFER RIBONUCLEIC ACID (YEAST, PHE)


Mass: 24890.121 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: TERNARY COMPLEX WITH GUANOSINE-5'-(BETA,GAMMA-IMIDO) TRIPHOSPHATE (GDPNP)
#2: Protein OF ELONGATION FACTOR TU (EF-TU)


Mass: 44742.980 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / Strain: YT-1 / References: UniProt: Q01698

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Non-polymers , 4 types, 62 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsA NON-VERIFIED MG 2+ ION WAS INCLUDED IN ALL THREE TRNA MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown / Details: Nissen, P., (1994) FEBS Lett., 356, 165. / PH range low: 7 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlTC1drop
247-49 %AS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 80769 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
RefinementResolution: 2.7→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.29 -5 %
Rwork0.206 --
all-76349 -
obs-76349 91.1 %
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9432 4956 135 50 14573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.63
X-RAY DIFFRACTIONt_dihedral_angle_d17.3
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.01
X-RAY DIFFRACTIONt_it6.12
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.206 / Rfactor Rfree: 0.296
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.3
X-RAY DIFFRACTIONt_plane_restr0.01

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