2AHO | pdb_00002aho

Structure of the archaeal initiation factor eIF2 alpha-gamma heterodimer from Sulfolobus solfataricus complexed with GDPNP

PDB DOI: https://doi.org/10.2210/pdb2AHO/pdb

Classification: TRANSLATION
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-07-28 Released: 2006-01-31
Deposition Author(s): Yatime, L., Mechulam, Y., Blanquet, S., Schmitt, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.291 (Depositor)
R-Value Work:
0.224 (Depositor), 0.233 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Literature

Structural Switch of the gamma Subunit in an Archaeal aIF2alphagamma Heterodimer

Yatime, L., Mechulam, Y., Blanquet, S., Schmitt, E.

(2006) Structure 14: 119-128

PubMed: 16407071 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2005.09.020
Primary Citation Related Structures:
2AHO

PubMed Abstract:
Eukaryotic and archaeal initiation factors 2 (e/aIF2) are heterotrimeric proteins (alphabetagamma) supplying the small subunit of the ribosome with methionylated initiator tRNA. This study reports the crystallographic structure of an aIF2alphagamma heterodimer from Sulfolobus solfataricus bound to Gpp(NH)p-Mg(2+). aIF2gamma is in a closed conformation with the G domain packed on domains II and III. The C-terminal domain of aIF2alpha interacts with domain II of aIF2gamma. Conformations of the two switch regions involved in GTP binding are similar to those encountered in an EF1A:GTP:Phe-tRNA(Phe) complex. Comparison with the EF1A structure suggests that only the gamma subunit of the aIF2alphagamma heterodimer contacts tRNA. Because the alpha subunit markedly reinforces the affinity of tRNA for the gamma subunit, a contribution of the alpha subunit to the switch movements observed in the gamma structure is considered.

Organizational Affiliation

Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France.

Macromolecule Content

Total Structure Weight: 76.76 kDa
Atom Count: 5,253
Modeled Residue Count: 660
Deposited Residue Count: 680
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor 2 gamma subunit	A	414	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.6.5.3
UniProt
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980A5 Go to UniProtKB: Q980A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q980A5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor 2 alpha subunit	B	266	Saccharolobus solfataricus	Mutation(s): 0
UniProt
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Z79 Go to UniProtKB: Q97Z79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97Z79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.291 (Depositor)
R-Value Work: 0.224 (Depositor), 0.233 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.6	α = 90
b = 112.9	β = 90
c = 194.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
PHASER	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-01-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description