PDB-3izq: Structure of the Dom34-Hbs1-GDPNP complex bound to a tr...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3izq
Title	Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome
Descriptor	Protein DOM34 (E.C.3.1.-.-) Elongation factor 1 alpha-like protein
Keywords	RIBOSOMAL PROTEIN, HYDROLASE, No-Go mRNA decay
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-1811, Made by Jmol #3: With PDB-, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1811 PDB-3izb PDB-3ize PDB-3izf PDB-3izs
Similar strucutres (beta)	Diagram EMDB-1646 EMDB-5603 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nat.Struct.Mol.Biol., Vol. 18, Page: 715 - 720, Year: 2011,
Title	Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
Authors	Becker, T., Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Sieber, H., Motaal, B.A., Mielke, T., Berninghausen, O., Beckmann, R.
Links	DOI: 10.1038/nsmb.2057

Components
ID 1 : Dom34p
Image
Description	Protein DOM34
Type	polypeptide(L)
Formula weight	44120.262 Da
Number of molecules	1
ID	1
Ec	3.1.-.-
Source	Method: Isolated from a genetically manipulated source Gene: brewer's yeast,lager beer yeast,yeast, DOM34, N2016, YNL001W, ID:4932, Saccharomyces cerevisiae Host: ID:562, Escherichia coli , pET21a
Links	UniProt: P33309, Sequence view
ID 2 : Hbs1p
Image
Description	Elongation factor 1 alpha-like protein
Type	polypeptide(L)
Formula weight	68827.094 Da
Number of molecules	1
ID	2
Source	Method: Isolated from a genetically manipulated source Gene: yeast, HBS1, YKR084C, YKR404, ID:4932, Saccharomyces cerevisiae Host: ID:562, Escherichia coli, pET28b
Links	UniProt: P32769, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	Ribosome-bound Dom34-Hbs1-GDPNP complex
Entity assembly
Assembly-ID	1
Name	No-Go mRNA decay factor
Entity assembly
Assembly-ID	1
Name	No-Go mRNA decay factor
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.0
Sample concentration	0.02 mg/ml
Sample support
Details	Carbon-coated Quantifoil with 2 nm carbon on top
Vitrification
Cryogen name	ETHANE
Details	Blotted for 10 seconds before plunging, used 2 layer of filter paper
Humidity	100
Instrument	Vitrobot
Experiment
Method	ELECTRON MICROSCOPY

Processing
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
Actual pixel size	1.2375 A/pix
Method	Single particle projection-matching
Nominal pixel size	1.2375 A/pix
Resolution	9.5 A
Software	Spider
3D fitting
Refinement Space	REAL
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	7183
Protein atoms	7183