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- PDB-3qsy: Recognition of the methionylated initiator tRNA by the translatio... -

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Basic information

Entry
Database: PDB / ID: 3qsy
TitleRecognition of the methionylated initiator tRNA by the translation initiation factor 2 in Archaea
Components
  • Translation initiation factor 2 subunit alpha
  • Translation initiation factor 2 subunit gamma
  • tRNA
KeywordsTRANSLATION/RNA / translation initiation / archaea / e/aIF2 / tRNAi / G-protein / GTP Binding / Met-tRNAi Binding / Ribosome Binding / mRNA Binding / Ribosome / TRANSLATION-RNA complex
Function / homology
Function and homology information


selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / GTP binding / RNA binding / metal ion binding / cytosol
Similarity search - Function
EIF_2_alpha / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, gamma subunit / 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 ...EIF_2_alpha / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, gamma subunit / 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 / Translation factors / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Elongation factor Tu domain 2 / S1 RNA binding domain / S1 domain / 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 / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / : / RNA / RNA (> 10) / 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: 3.2 Å
AuthorsNikonov, O.S. / Stolboushkina, E.A. / Zelinskaya, N.V. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met.)
Authors: Stolboushkina, E. / Nikonov, S. / Zelinskaya, N. / Arkhipova, V. / Nikulin, A. / Garber, M. / Nikonov, O.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
D: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2015
Polymers80,5293
Non-polymers6712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-31 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.680, 93.680, 220.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 45849.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5
#2: Protein Translation initiation factor 2 subunit alpha / aIF2-alpha / eIF-2-alpha


Mass: 9893.411 Da / Num. of mol.: 1 / Fragment: domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z79
#3: RNA chain tRNA


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Met-tRNAi from Escherichia coli(unmodified bases) / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 312135
#4: 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
#5: 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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 45% ammonium sulphate, 30mM Tris-HCl, 5mM MES, 7mM MgCl2, 0.5mM DTT, 0.2mM GDPNP, 300mM NDSB 195, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

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Data collection

DiffractionMean temperature: 198.3 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3→25 Å / Num. all: 23160 / Num. obs: 23068 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3-3.1199.9
3.1-3.15199.9
3.15-3.21100
3.2-3.25199.8
3.25-3.31100
3.3-3.41100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHO

2aho


Resolution: 3.2→14.95 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2.1 / Phase error: 39.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 940 5.32 %RANDOM
Rwork0.2783 16744 --
obs0.2786 17676 93.31 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 128.162 Å2 / ksol: 0.138 e/Å3
Displacement parametersBiso max: 544.83 Å2 / Biso mean: 129.8513 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1--54.4318 Å20 Å20 Å2
2---54.4318 Å20 Å2
3---108.8636 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 1639 40 0 5593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095861
X-RAY DIFFRACTIONf_angle_d1.3078298
X-RAY DIFFRACTIONf_chiral_restr0.0871025
X-RAY DIFFRACTIONf_plane_restr0.006759
X-RAY DIFFRACTIONf_dihedral_angle_d19.9682449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2004-3.36730.34551300.30242251238185
3.3673-3.57550.32221330.25762284241786
3.5755-3.8470.31491150.27692278239386
3.847-4.2260.30091470.28422326247387
4.226-4.8190.31311390.28992415255490
4.819-6.00340.30151210.29682539266093
6.0034-14.80920.27891340.25852651278593
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02930.0060.00310.0165-0.03480.04780.13020.0175-0.042-0.0688-0.03960.00790.02420.06060.1191-0.009-0.1728-0.14630.00050.0430.040429.0436-16.764710.0304
20.03-0.0009-0.0290.01710.0210.04330.07410.06870.0058-0.0395-0.14030.03280.00260.055-0.0240.12980.0203-0.04690.16960.07680.172825.9517-7.518619.5164
30.1084-0.0499-0.00020.03270.00970.0244-0.0147-0.0241-0.0128-0.0011-0.01380.0216-0.0390.0369-0.02250.0380.0252-0.10090.01660.11890.203819.3892-14.517226.698
40.02410.02460.02760.01450.01360.06390.0929-0.02790.00590.01260.05410.0673-0.11790.0440.0580.3127-0.2930.0820.17480.10340.243132.875910.570715.3915
5-0.00230.0054-0.00240.02820.01110.0249-0.00370.02820.0183-0.03140.07690.0068-0.0036-0.00270.07480.1370.1760.069-0.0232-0.05410.054230.141922.871418.9469
60.008-0.0224-0.03210.05240.0060.06690.06350.0321-0.0011-0.0898-0.0017-0.0045-0.0922-0.02710.06660.1215-0.0187-0.03640.20530.02570.086929.059616.379222.2211
70.0323-0.004-0.01070.01850.03330.02880.04340.0691-0.02630.09190.1712-0.02030.10660.05510.1359-0.00770.031-0.2480.1549-0.07160.011116.443214.436238.1217
80.07170.0752-0.09080.1354-0.03280.17370.0365-0.0017-0.0174-0.03080.0622-0.0323-0.0559-0.01750.08840.272-0.0121-0.07810.1263-0.0990.292455.252233.953124.1529
90.00040.00140.0009-0.0001-0.00070.0018-0.01450.00820.0011-0.0046-0.01720.0002-0.03310.005400.4879-0.0257-0.05470.5143-0.18350.417351.086233.29548.9373
100.01060.02570.00870.06040.01610.04490.012-0.08930.00250.0502-0.0520.00920.0258-0.0973-0.02320.114-0.00050.00350.150.01310.072361.88229.930120.3065
110.00230.0057-00.0157-0.00050.00020.0009-0.00870.0110.00810.00570.0007-0.0175-0.00590.0060.10240.0008-0.01490.1123-0.02550.099874.40532.633821.5625
120.0309-0.00650.01610.0177-0.01360.01610.04340.0121-0.01640.04670.03650.0055-0.00490.0170.02460.27490.040.05660.055-0.06170.178756.753241.094919.7819
130.03170.02050.00960.00540.00210.1906-0.10540.01780.03790.01040.0203-0.0121-0.11290.0505-0.02660.2820.0162-0.15320.2481-0.0370.618744.425220.721342.4956
140.0007-0.0008-0.0007-0.0007-0.00350.00030.0131-0.01450.00060.09260.03320.0129-0.0089-0.00310.00010.45070.0228-0.07830.2369-0.05220.318423.91315.826168.7667
150.0011-0.00020.0005-0.0002-0.0011-0.00030.0050.0087-0.01320.02680.01820.0039-0.0351-0.0153-00.7496-0.0341-0.11580.7304-0.00960.60823.529318.650763.2442
160.06260.02910.01560.03560.04110.0876-0.0489-0.0990.04550.07350.0279-0.01680.086-0.0511-0.02520.18530.06180.05350.16860.06230.333357.302319.734546.9014
170.00040.00250.00630.0624-0.06620.0796-0.0315-0.01750.0179-0.0584-0.0747-0.0505-0.06210.0009-0.08460.2243-0.00590.10630.15790.00030.123231.69054.060533.2936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:81 )A1 - 81
2X-RAY DIFFRACTION2( CHAIN A AND RESID 82:127 )A82 - 127
3X-RAY DIFFRACTION3( CHAIN A AND RESID 128:198 )A128 - 198
4X-RAY DIFFRACTION4( CHAIN A AND RESID 199:238 )A199 - 238
5X-RAY DIFFRACTION5( CHAIN A AND RESID 239:278 )A239 - 278
6X-RAY DIFFRACTION6( CHAIN A AND RESID 279:338 )A279 - 338
7X-RAY DIFFRACTION7( CHAIN A AND RESID 339:415 )A339 - 415
8X-RAY DIFFRACTION8( CHAIN B AND RESID 176:190 )B176 - 190
9X-RAY DIFFRACTION9( CHAIN B AND RESID 191:207 )B191 - 207
10X-RAY DIFFRACTION10( CHAIN B AND RESID 208:231 )B208 - 231
11X-RAY DIFFRACTION11( CHAIN B AND RESID 232:237 )B232 - 237
12X-RAY DIFFRACTION12( CHAIN B AND RESID 238:264 )B238 - 264
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:24 )D1 - 24
14X-RAY DIFFRACTION14( CHAIN D AND RESID 25:34 )D25 - 34
15X-RAY DIFFRACTION15( CHAIN D AND RESID 35:44 )D35 - 44
16X-RAY DIFFRACTION16( CHAIN D AND RESID 45:69 )D45 - 69
17X-RAY DIFFRACTION17( CHAIN D AND RESID 70:77 )D70 - 77

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