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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "RAT8"

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Search Summary

This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Saccharomyces cerevisiae (9)
	Saccharomyces cerevisiae YJM789 (1)

Taxonomy

Eukaryota (10)

Experimental Method

	X-RAY DIFFRACTION (8)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (10)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (3)
	2.0 - 2.5 (1)
	2.5 - 3.0 (2)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (6)
	2015 - 2019 (1)

Enzyme Classification Name

Hydrolases (10)

Symmetry Type

Asymmetric (10)

SCOP Classification

	Alpha and beta proteins (a/b) (9)
	All beta proteins (1)
	Artifacts (1)

AllSelected

1 to 10 of 10 Structures

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2KBE \| pdb_00002kbe	Download File View File

solution structure of amino-terminal domain of Dbp5p

Fan, J.S., Zhang, J., Yang, D.

(2009) J Mol Biology 388: 1-10

Released	2009-10-13
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein)

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2KBF \| pdb_00002kbf	Download File View File

solution structure of carboxyl-terminal domain of Dbp5p

Fan, J.S., Zhang, J., Yang, D.

(2009) J Mol Biology 388: 1-10

Released	2009-10-13
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein)

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3GFP \| pdb_00003gfp	Download File View File

Structure of the C-terminal domain of the DEAD-box protein Dbp5

Erzberger, J.P., Dossani, Z.Y., Weirich, C.S., Weis, K., Berger, J.M.

(2009) Proc Natl Acad Sci U S A 106: 16251-16256

Released	2009-09-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	DEAD box protein 5 (protein)

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3PEU \| pdb_00003peu	Download File View File

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-03-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) Nucleoporin GLE1 (protein)
Unique Ligands	GOL, IHP, SO4

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3PEV \| pdb_00003pev	Download File View File

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-03-23
Method	X-RAY DIFFRACTION 2.499 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) Nucleoporin GLE1 (protein)
Unique Ligands	GOL, IHP, SO4

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3PEW \| pdb_00003pew	Download File View File

S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-03-23
Method	X-RAY DIFFRACTION 1.501 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) RNA (5'-R(PUPUPUPUPUPU)-3') (nucleic acid)
Unique Ligands	ADP, BEF, MG, NO3

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3PEY \| pdb_00003pey	Download File View File

S. cerevisiae Dbp5 bound to RNA and ADP BeF3

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-03-23
Method	X-RAY DIFFRACTION 1.401 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) RNA (5'-R(PUPUPUPUPUPU)-3') (nucleic acid)
Unique Ligands	ADP, BEF, GOL, MG, NO3

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3RRM \| pdb_00003rrm	Download File View File

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-05-18
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) Nucleoporin GLE1 (protein) Nucleoporin NUP159 (protein)
Unique Ligands	ADP, IHP, MG

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3RRN \| pdb_00003rrn	Download File View File

S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6

Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

(2011) Nature 472: 238-242

Released	2011-05-18
Method	X-RAY DIFFRACTION 4.001 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) Nucleoporin GLE1 (protein)
Unique Ligands	ADP, IHP

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5ELX \| pdb_00005elx	Download File View File

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

Merchant, M.K., Modis, Y.

(2016) J Mol Biology 428: 492-508

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Saccharomyces cerevisiae YJM789
Macromolecule	ATP-dependent RNA helicase DBP5 (protein) RNA (5'-R(PUPUPUPUPUPU)-3') (nucleic acid)
Unique Ligands	BEF, M2A, MG, NO3

1 to 10 of 10 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2KBE | pdb_00002kbe

solution structure of amino-terminal domain of Dbp5p

2KBF | pdb_00002kbf

solution structure of carboxyl-terminal domain of Dbp5p

3GFP | pdb_00003gfp

Structure of the C-terminal domain of the DEAD-box protein Dbp5

3PEU | pdb_00003peu

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6

3PEV | pdb_00003pev

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6

3PEW | pdb_00003pew

S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3

3PEY | pdb_00003pey

S. cerevisiae Dbp5 bound to RNA and ADP BeF3

3RRM | pdb_00003rrm

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp

3RRN | pdb_00003rrn

S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6

5ELX | pdb_00005elx

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2KBE | pdb_00002kbe

2KBF | pdb_00002kbf

3GFP | pdb_00003gfp

3PEU | pdb_00003peu

3PEV | pdb_00003pev

3PEW | pdb_00003pew

3PEY | pdb_00003pey

3RRM | pdb_00003rrm

3RRN | pdb_00003rrn

5ELX | pdb_00005elx