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- PDB-3v11: Structure of the ternary initiation complex AIF2:GDPNP:methionyla... -

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Basic information

Entry
Database: PDB / ID: 3v11
TitleStructure of the ternary initiation complex AIF2:GDPNP:methionylated initiator TRNA
Components
  • (Translation initiation factor 2 subunit ...) x 3
  • Initiator tRNA
KeywordsTRANSLATION/RNA / GTP binding module / initiator tRNA carrier / GTP and tRNA / TRANSLATION-RNA complex
Function / homology
Function and homology information


selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / mRNA binding / GTP binding / RNA binding / metal ion binding / cytosol
Similarity search - Function
Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / IF2a, S1-like domain ...Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Translation initiation factor 2, gamma subunit / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Elongation factor Tu domain 2 / S1 RNA binding domain / S1 domain / 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / Translation initiation factor 2 subunit beta / Translation initiation factor 2 subunit alpha / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsMechulam, Y. / Schmitt, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA.
Authors: Schmitt, E. / Panvert, M. / Lazennec-Schurdevin, C. / Coureux, P.D. / Perez, J. / Thompson, A. / Mechulam, Y.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
A: Translation initiation factor 2 subunit gamma
B: Translation initiation factor 2 subunit alpha
C: Translation initiation factor 2 subunit beta
D: Initiator tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4917
Polymers116,7954
Non-polymers6963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-51 kcal/mol
Surface area42330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.000, 133.000, 167.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Translation initiation factor 2 subunit ... , 3 types, 3 molecules ABC

#1: Protein Translation initiation factor 2 subunit gamma / aIF2-gamma / eIF-2-gamma


Mass: 45718.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2g, SSO0412 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta pLacIRARE / References: UniProt: Q980A5
#2: Protein Translation initiation factor 2 subunit alpha / aIF2-alpha / eIF-2-alpha


Mass: 30432.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2a, SSO1050 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta pLacIRARE / References: UniProt: Q97Z79
#3: Protein Translation initiation factor 2 subunit beta / aIF2-beta / eIF-2-beta


Mass: 15811.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2b, SSO2381 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta pLacIRARE / References: UniProt: Q97W59

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RNA chain , 1 types, 1 molecules D

#4: RNA chain Initiator tRNA


Mass: 24832.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 5% PEG 20 000, 50mM MES 5.7, 200mM KCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.12713 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2011
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 5→115 Å / Num. all: 7664 / Num. obs: 7664 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 340.45 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066
Reflection shellResolution: 5→5.2 Å / Redundancy: 6.52 % / Rmerge(I) obs: 0.847 / Rsym value: 0.847 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHO and 3CW5

2aho

3cw5


Resolution: 5→47.426 Å / SU ML: 1.45 / σ(F): 1.35 / Phase error: 39.9 / Stereochemistry target values: ML
Details: THE AUTHORS STATE THAT POSITIONING OF BASES 73-76 OF THE TRNA IS TENTATIVE
RfactorNum. reflection% reflection
Rfree0.3438 358 4.69 %
Rwork0.2622 --
obs0.2654 7627 98.59 %
all-7627 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 210.252 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-196.2964 Å20 Å2-0 Å2
2--196.2964 Å2-0 Å2
3----5.9758 Å2
Refinement stepCycle: LAST / Resolution: 5→47.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 1624 41 0 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017246
X-RAY DIFFRACTIONf_angle_d1.55710167
X-RAY DIFFRACTIONf_dihedral_angle_d21.0962958
X-RAY DIFFRACTIONf_chiral_restr0.0941234
X-RAY DIFFRACTIONf_plane_restr0.007990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.0004-5.72290.42681340.38132368X-RAY DIFFRACTION99
5.7229-7.20610.43081190.28542398X-RAY DIFFRACTION99
7.2061-47.42860.31671050.24852503X-RAY DIFFRACTION98

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