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- PDB-3cw2: Crystal structure of the intact archaeal translation initiation f... -

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Basic information

Entry
Database: PDB / ID: 3cw2
TitleCrystal structure of the intact archaeal translation initiation factor 2 from Sulfolobus solfataricus .
Components
  • Translation initiation factor 2 subunit alphaInitiation factor
  • Translation initiation factor 2 subunit betaInitiation factor
  • Translation initiation factor 2 subunit gammaInitiation factor
KeywordsTRANSLATION / AIF2 / INTACT AIF2 / INITIATION FACTOR 2 ALPHA SUBUNIT / INITIATION FACTOR 2 BETA SUBUNIT / INITIATION FACTOR 2 GAMMA SUBUNIT / INITIATION OF THE TRANSLATION / Initiation factor / Protein biosynthesis / RNA-binding / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / translation elongation factor activity / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / GTP binding ...protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / 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
Similarity search - Function
EIF_2_alpha / Translation initiation factor 2; subunit 1; domain 2 / 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 ...EIF_2_alpha / Translation initiation factor 2; subunit 1; domain 2 / 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 / Translation factors / S1 domain profile. / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStolboushkina, E.A. / Nikonov, S.V. / Nikulin, A.D. / Blaesi, U. / Manstein, D.J. / Fedorov, R.V. / Garber, M.B. / Nikonov, O.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the intact archaeal translation initiation factor 2 demonstrates very high conformational flexibility in the alpha- and beta-subunits.
Authors: Stolboushkina, E. / Nikonov, S. / Nikulin, A. / Blasi, U. / Manstein, D.J. / Fedorov, R. / Garber, M. / Nikonov, O.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 2 subunit gamma
B: Translation initiation factor 2 subunit gamma
C: Translation initiation factor 2 subunit alpha
D: Translation initiation factor 2 subunit alpha
K: Translation initiation factor 2 subunit beta
L: Translation initiation factor 2 subunit beta
E: Translation initiation factor 2 subunit gamma
F: Translation initiation factor 2 subunit gamma
G: Translation initiation factor 2 subunit alpha
H: Translation initiation factor 2 subunit alpha
M: Translation initiation factor 2 subunit beta
N: Translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)368,89712
Polymers368,89712
Non-polymers00
Water0
1
A: Translation initiation factor 2 subunit gamma
C: Translation initiation factor 2 subunit alpha
K: Translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)92,2243
Polymers92,2243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-24 kcal/mol
Surface area42710 Å2
MethodPISA
2
B: Translation initiation factor 2 subunit gamma
D: Translation initiation factor 2 subunit alpha
L: Translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)92,2243
Polymers92,2243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-18 kcal/mol
Surface area34770 Å2
MethodPISA
3
E: Translation initiation factor 2 subunit gamma
G: Translation initiation factor 2 subunit alpha
M: Translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)92,2243
Polymers92,2243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area43930 Å2
MethodPISA
4
F: Translation initiation factor 2 subunit gamma
H: Translation initiation factor 2 subunit alpha
N: Translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)92,2243
Polymers92,2243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-21 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.200, 162.920, 161.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4 / Fragment: aIF2gamma subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g, SSO0412 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5
#2: Protein
Translation initiation factor 2 subunit alpha / Initiation factor / eIF-2-alpha / aIF2-alpha


Mass: 30432.355 Da / Num. of mol.: 4 / Fragment: aIF2alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2a, SSO1050 / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97Z79
#3: Protein
Translation initiation factor 2 subunit beta / Initiation factor / eIF-2-beta / aIF2-beta


Mass: 15942.740 Da / Num. of mol.: 4 / Fragment: aIF2beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2b, SSO2381 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W59

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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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 0.72M sodium formate, 9% PEG 8000, 9% PEG 1000, 1% monomethyl ether polyethylene glycol 5000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 2007
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.459
ReflectionResolution: 2.8→19.913 Å / Num. all: 98811 / Num. obs: 95812 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.16 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.71
Reflection shellResolution: 2.8→2.85 Å / % possible all: 90.9

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Processing

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

2plf


Resolution: 2.8→19.9118 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4941 -RANDOM
Rwork0.225 ---
all-98811 --
obs-95812 92 %-
Displacement parametersBiso mean: 71.899 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.9118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23824 0 0 0 23824

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