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- PDB-3i1f: Gamma-subunit of the translation initiation factor 2 from S. solf... -

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Basic information

Entry
Database: PDB / ID: 3i1f
TitleGamma-subunit of the translation initiation factor 2 from S. solfataricus in complex with Gpp(CH2)p
ComponentsTranslation initiation factor 2 subunit gammaInitiation factor
KeywordsTRANSLATION / aIF2 / Initiation factor 2 gamma subunit / Initiation of the translation / nucleotide binding / GDPCP / mRNA binding / GTP-binding / Initiation factor / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Translation initiation factor 2, gamma 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 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...Translation initiation factor 2, gamma 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 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / PHOSPHATE ION / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStolboushkina, E.A. / Nikonov, S.V. / Nikulin, A.D. / Blaesi, U. / Garber, M.B. / Nikonov, O.S.
CitationJournal: To be Published
Title: 5-prime-triphosphate end of mRNA recognizes the second GTP-binding site on the gamma-subunit of the archaeal translation initiation factor 2
Authors: Stolboushkina, E.A. / Nikonov, S.V. / Nikulin, A.D. / Blaesi, U. / Garber, M.B. / Nikonov, O.S.
History
DepositionJun 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1218
Polymers91,6982
Non-polymers1,4226
Water6,431357
1
A: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5604
Polymers45,8491
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5604
Polymers45,8491
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.770, 95.770, 165.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 45849.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(de3) / References: UniProt: Q980A5
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 4.77 Å3/Da / Density % sol: 74.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% natrium malonate dihydrate, 50mM glycine, 3mM CdCl2 at the protein/nucleotide molar ratio 1/10. For cryoprotection ethylene glycol was added to the reservoir solution at the final ...Details: 15% natrium malonate dihydrate, 50mM glycine, 3mM CdCl2 at the protein/nucleotide molar ratio 1/10. For cryoprotection ethylene glycol was added to the reservoir solution at the final concentration of 15% (v/v), pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 203.3 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2007 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.5→19.4 Å / Num. all: 58626 / Num. obs: 57747 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.83 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.73
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.78 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6449 / % possible all: 98.7

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PMD

2pmd


Resolution: 2.5→19.4 Å / Cross valid method: THROUGHOUT / σ(F): 1.97 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 2908 5.04 %RANDOM
Rwork0.2261 ---
obs0.2281 57741 98.69 %-
all-58619 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 118.052 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6426 0 84 357 6867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54310.29761460.29722768X-RAY DIFFRACTION94
2.5431-2.58920.29211460.3012765X-RAY DIFFRACTION94
2.5892-2.63880.32621430.29492718X-RAY DIFFRACTION94
2.6388-2.69250.30781440.29822744X-RAY DIFFRACTION94
2.6925-2.75090.28061460.29282764X-RAY DIFFRACTION94
2.7509-2.81470.35181450.28832762X-RAY DIFFRACTION94
2.8147-2.88480.33551440.28282738X-RAY DIFFRACTION94
2.8848-2.96250.29351450.27782750X-RAY DIFFRACTION94
2.9625-3.04930.32091430.26932730X-RAY DIFFRACTION94
3.0493-3.14720.30981450.26912747X-RAY DIFFRACTION94
3.1472-3.25910.27011450.26732758X-RAY DIFFRACTION94
3.2591-3.38880.28581470.25372792X-RAY DIFFRACTION94
3.3888-3.5420.27131450.23652760X-RAY DIFFRACTION95
3.542-3.72730.36971430.29132701X-RAY DIFFRACTION93
3.7273-3.95860.29781440.23252737X-RAY DIFFRACTION93
3.9586-4.26070.25921450.22192757X-RAY DIFFRACTION94
4.2607-4.6830.18371430.1642726X-RAY DIFFRACTION94
4.683-5.34590.21331460.16562777X-RAY DIFFRACTION94
5.3459-6.68080.28061440.18612738X-RAY DIFFRACTION94
6.6808-18.34830.16761380.14292603X-RAY DIFFRACTION89
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)
10.4445-0.22440.00020.8397-0.3751.54830.128-0.0429-0.0656-0.0103-0.28740.0927-0.7568-0.18730.15540.78820.0336-0.0361.2558-0.04470.430646.5586-32.1053-2.4265
20.3347-0.0988-0.05620.0519-0.05241.7723-0.13240.3770.02010.27340.0362-0.00710.0208-0.06090.08090.80310.071-0.01620.9470.02250.6064.5543-56.459214.2712
30.6555-0.4645-0.51790.35130.3940.4726-0.0645-0.05250.0413-0.0026-0.00470.0004-0.0661-0.0640.05962.53280.2585-0.23972.4509-0.13152.34712.5621-44.683234.9194
41.2199-0.18140.54780.1362-0.01180.4374-0.0226-0.019-0.0168-0.0112-0.06940.07110.003-0.09320.08922.42410.1950.00553.014-0.42672.540338.2209-49.9325-5.7449
50.64650.5687-0.14332.77191.36871.2778-1.22960.7929-1.68740.30070.18350.19220.3877-0.35810.96570.70690.58190.18780.53520.34490.685622.1877-50.80934.4547
60.3218-0.14150.06230.26980.26330.4309-0.22630.4197-0.2359-0.03330.1830.009-0.3908-0.29930.01911.22520.06450.05041.9387-0.13261.023832.2696-42.1513-8.7862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A 2-415A2 - 415
2X-RAY DIFFRACTION2chain B 2-415B2 - 415
3X-RAY DIFFRACTION3chain B 1B1
4X-RAY DIFFRACTION4chain A 1A1
5X-RAY DIFFRACTION5chain A 416, chain B 416, 417
6X-RAY DIFFRACTION6chain A 417, 418, chain B 418, 419

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