PDB-2p8y: Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDP:sordarin c...

Basic information

• Entry: Database: PDB / ID: 2p8y
• Title: Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDP:sordarin cryo-EM reconstruction
• Components: Elongation factor 2
• Keywords: TRANSLATION / elongation / translocation / GTPase / 80S ribosome

Function / homology

Function:

Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol

Domain/homology:

Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase

Component:

ADENOSINE-5-DIPHOSPHORIBOSE / GUANOSINE-5'-DIPHOSPHATE / Chem-SO1 / Elongation factor 2

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
• Authors: Taylor, D.J. / Nilsson, J. / Merrill, A.R. / Andersen, G.R. / Nissen, P. / Frank, J.
• Citation: Journal: EMBO J / Year: 2007; Title: Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.; Authors: Derek J Taylor / Jakob Nilsson / A Rod Merrill / Gregers Rom Andersen / Poul Nissen / Joachim Frank / ; Abstract: On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit.

History

Deposition	Mar 23, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 18, 2018	Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4	Dec 18, 2019	Group: Database references / Derived calculations / Other Category: atom_sites / cell / struct_conn / struct_ref_seq_dif Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Assembly

Deposited unit

T: Elongation factor 2

hetero molecules

Summary:

• 95 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	95,046	4
Polymers	93,549	1
Non-polymers	1,497	3
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

Components

#1: Protein

T Elongation factor 2 / EF-2 / Translation elongation factor 2 / Eukaryotic elongation factor 2 / eEF2 / Ribosomal translocase

Details:

Mass: 93549.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324

#2: Chemical

T-1699 ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE

Details:

Mass: 559.316 Da / Num. of mol.: 1 /