PDB-2p8x: Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPN...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2p8x
Title	Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPNP cryo-EM reconstruction
Descriptor	Elongation factor 2 Elongation factor Tu-B
Keywords	TRANSLATION, elongation, translocation, GTPase, 80S ribosome
Authors	Taylor, D.J., Nilsson, J., Merrill, A.R., Andersen, G.R., Nissen, P., Frank, J.
Date	Deposition: 2007-03-23, Release: 2007-05-08
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1343, Made by Jmol #3: Superimposing with simplified surface model of EM map, EMDB-1345, Made by Jmol #4: Superimposing with EM 3D map: EMDB-1343, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1343 CiteFit EMDB-1345 CiteFit EMDB-1342 Cite EMDB-1344 Cite PDB-2p8w Cite PDB-2p8y Cite PDB-2p8z Cite PDB-1k5x PDB-1k5y Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-2p8w PDB-2p8y PDB-2p8z EMDB-1364 PDB-2ix8 PDB-1kju List of similar structure data about Omokage system

Article
Citation - primary
Article	EMBO J., Vol. 26, Issue 9, Page 2421-31, 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 Howard Hughes Medical Institute, Health Research Inc.,Wadsworth Center, Albany, NY 12201-0509, USA.
Keywords	Adenosine Diphosphate (metabolism, 58-64-0), Ascomycota (metabolism), Cryoelectron Microscopy (methods), Guanosine Triphosphate (chemistry, 86-01-1), Hydrolysis, Models, Molecular, Molecular Sequence Data, Peptide Elongation Factor 2 (chemistry), Peptide Elongation Factor G (chemistry), Protein Structure, Tertiary, RNA Transport, RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry)
Links	DOI: 10.1038/sj.emboj.7601677, PubMed: 17446867, PMC: PMC1864975

Components
ID 1 : EF-2, Translation elongation factor 2, Eukaryotic elongation factor 2, eEF2, Ribosomal translocase
Image
Description	Elongation factor 2
Type	polymer
Formula weight	93550.094 Da
Number of molecules	1
Source	Method: Isolated from a natural source Common name: baker's yeast Genus: Saccharomyces NCBI taxonomy: ID:4932 Organism scientific: Saccharomyces cerevisiae
Links	UniProt: P32324, Sequence view
ID 2 : EF-Tu-B
Image
Description	Elongation factor Tu-B
Type	polymer
Fragment	SWITCH 1 LOOP
Formula weight	3829.162 Da
Number of molecules	1
Source	Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274 Organism scientific: Thermus thermophilus
Links	UniProt: P60339, Sequence view
ID 3 : ADENOSINE-5-DIPHOSPHORIBOSE
Image
Description	ADENOSINE-5-DIPHOSPHORIBOSE
Type	non-polymer
Formula weight	559.319 Da
Number of molecules	1
Source	Method: Obtained synthetically
ID 4 : PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Image
Description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Type	non-polymer
Formula weight	522.198 Da
Number of molecules	1
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	PARTICLE
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.5
Sample concentration	0.096 mg/ml
Sample support
Details	Quantifoil holey-Carbon film grids
Vitrification
Details	rapid-freezing in liquid ethane

Processing
2D projection selection
Software name	TNT implementation of RSRef
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
Actual pixel size	1.86 A/pix
CTF correction method	CTF correction of 3D-maps by Wiener filtration
Details	SPIDER package
Magnification calibration	TMV
Method	3D projection matching, conjugate gradients with regularization
Nominal pixel size	1.86 A/pix
Resolution	9.7 A
3D fitting
Method	Real-space refinement using rigid bodies
Temperature factor	15
Refinement Protocol	TNT implementation of RSRef
Refinement Space	REAL
Software name	TNT implementation of RSRef
Target criteria	Maximization of correlation-coefficient
Refine hist
Total atoms	6677
Ligand atoms	67
Protein atoms	6610

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Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 2.6 MB .webm (WebM/VP8 format), 3.5 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.3 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB