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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yefanov, O."

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Search Summary

This query matches 39 Structures.

Refinements

Structure Determination Methodology

experimental (39)

Scientific Name of Source Organism

	synthetic construct (14)
	Homo sapiens (7)
	Mus musculus (4)
	Dengue virus (2)
	Neurospora (2)
	Bacillus subtilis (1)
	Canis lupus familiaris (1)
	Pea enation mosaic virus 2 (1)
	Schistosoma mansoni (1)
	Triticum aestivum (1)

More...

Taxonomy

	Eukaryota (15)
	other sequences (14)
	Bacteria (3)
	Riboviria (3)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (34)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

	RNA (39)
	Protein (14)
	DNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (7)
	2.5 - 3.0 (13)
	3.0 - 3.5 (10)
	3.5 - 4.0 (3)
	> 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (3)
	2005 - 2009 (1)
	2010 - 2014 (17)
	2015 - 2019 (5)
	2020 - 2024 (10)
	2025 - 2029 (2)

Enzyme Classification Name

	Transferases (1)
	Hydrolases (5)

Symmetry Type

	Asymmetric (12)
	Cyclic (2)

SCOP Classification

	Low resolution protein structures (1)
	All beta proteins (2)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 39 Structures

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1D4R \| pdb_00001d4r	Download File View File

29-mer fragment of human srp rna helix 6

Wild, K., Weichenrieder, O., Leonard, G.A., Cusack, S.

(1999) Structure 7: 1345-1352

Released	1999-12-02
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	29-MER OF MODIFIED SRP RNA HELIX 6 (nucleic acid)
Unique Ligands	MG

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1E8O \| pdb_00001e8o	Download File View File

Core of the Alu domain of the mammalian SRP

Weichenrieder, O., Wild, K., Strub, K., Cusack, S.

(2000) Nature 408: 167

Released	2000-11-08
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN (protein) SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (protein) 7SL RNA (nucleic acid)
Unique Ligands	SO4

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1RY1 \| pdb_00001ry1	Download File View File

Structure of the signal recognition particle interacting with the elongation-arrested ribosome

Halic, M., Becker, T., Pool, M.R., Spahn, C.M., Grassucci, R.A., Frank, J., Beckmann, R.

(2004) Nature 427: 808-814

Released	2004-04-20
Method	ELECTRON MICROSCOPY 12 Å
Organisms	Canis lupus familiaris Triticum aestivum
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 8

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1Y27 \| pdb_00001y27	Download File View File

G-riboswitch-guanine complex

Serganov, A., Yuan, Y.R., Patel, D.J.

(2004) Chem Biol 11: 1729-1741

Released	2004-12-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bacillus subtilis
Macromolecule	Bacillus subtilis xpt (nucleic acid)
Unique Ligands	GUN

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3DIY \| pdb_00003diy	Download File View File

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Mn2+ soak

Serganov, A.A.

(2008) Nature 455: 1263-1267

Released	2008-09-16
Method	X-RAY DIFFRACTION 2.71 Å
Macromolecule	RNA (174-MER) (nucleic acid)
Unique Ligands	K, LYS, MN, NA

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3KTV \| pdb_00003ktv	Download File View File

Crystal structure of the human SRP19/S-domain SRP RNA complex

Wild, K., Bange, G., Bozkurt, G., Sinning, I.

(2010) Acta Crystallogr D Biol Crystallogr 66: 295-303

Released	2010-02-16
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Homo sapiens
Macromolecule	Signal recognition particle 19 kDa protein (protein) SRP RNA (nucleic acid)
Unique Ligands	K, MG

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3NCU \| pdb_00003ncu	Download File View File

Structural and functional insights into pattern recognition by the innate immune receptor RIG-I

Sheng, G., Li, H.

(2010) Nat Struct Mol Biol 17: 781-787

Released	2010-06-30
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	RIG-I (protein) 5'-R((GDP)PAPCPGPCPUPAPGPCPGPUPC)-3' (nucleic acid)
Unique Ligands	ZN

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3OWI \| pdb_00003owi	Download File View File

Crystal structure of the glycine riboswitch bound to glycine

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.845 Å
Organisms	Vibrio cholerae MJ-1236
Macromolecule	Domain II of glycine riboswitch (nucleic acid)
Unique Ligands	GLY, MG

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3OWW \| pdb_00003oww	Download File View File

Crystal structure of the glycine riboswitch bound to glycine

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.802 Å
Macromolecule	domain II of glycine riboswitch (nucleic acid)
Unique Ligands	GLY, MG

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3OWZ \| pdb_00003owz	Download File View File

Crystal structure of glycine riboswitch, soaked in Iridium

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.949 Å
Macromolecule	Domain II of glycine riboswitch (nucleic acid)
Unique Ligands	GLY, IRI, MG

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3OX0 \| pdb_00003ox0	Download File View File

Crystal structure of glycine riboswitch, unbound state

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 3.049 Å
Macromolecule	Domain II of glycine riboswitch (nucleic acid)
Unique Ligands	MG

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3OXB \| pdb_00003oxb	Download File View File

Crystal structure of glycine riboswitch with single mutation

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.947 Å
Macromolecule	Domain II of glycine riboswitch (nucleic acid)
Unique Ligands	MG

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3OXD \| pdb_00003oxd	Download File View File

Crystal structure of glycine riboswitch with two mutations

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.999 Å
Macromolecule	domain II of glycine riboswitch (nucleic acid)
Unique Ligands	MG

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3OXE \| pdb_00003oxe	Download File View File

crystal structure of glycine riboswitch, Mn2+ soaked

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.899 Å
Macromolecule	domain II of glycine riboswitch (nucleic acid)
Unique Ligands	GLY, MG, MN

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3OXJ \| pdb_00003oxj	Download File View File

crystal structure of glycine riboswitch, soaked in Ba2+

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 3.2 Å
Macromolecule	domain II of glycine riboswitch (nucleic acid)
Unique Ligands	BA, GLY, MG

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3OXM \| pdb_00003oxm	Download File View File

crystal structure of glycine riboswitch, Tl-Acetate soaked

Huang, L., Serganov, A., Patel, D.J.

(2010) Mol Cell 40: 774-786

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.95 Å
Macromolecule	domain II of glycine riboswitch (nucleic acid)
Unique Ligands	GLY, MG, TL

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3ZD4 \| pdb_00003zd4	Download File View File

Full-Length Hammerhead Ribozyme with G12A substitution at the general base position

Scott, W.G., Schultz, E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2256

Released	2012-12-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	synthetic construct
Macromolecule	HAMMERHEAD RIBOZYME, ENZYME STRAND (nucleic acid) HAMMERHEAD RIBOZYME, SUBSTRATE STRAND (nucleic acid)

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3ZD5 \| pdb_00003zd5	Download File View File

THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME

Martick, M., Scott, W.G.

(2006) Cell 126: 309-320

Released	2012-12-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Schistosoma mansoni
Macromolecule	HAMMERHEAD RIBOZYME, ENZYME STRAND (nucleic acid) HAMMERHEAD RIBOZYME, SUBSTRATE STRAND (nucleic acid)

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3ZP8 \| pdb_00003zp8	Download File View File

HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME

Anderson, M., Schultz, E., Martick, M., Scott, W.G.

(2013) J Mol Biology 425: 3790

Released	2013-03-06
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	synthetic construct
Macromolecule	HAMMERHEAD RIBOZYME, ENZYME STRAND (nucleic acid) HAMMERHEAD RIBOZYME, SUBSTRATE STRAND (nucleic acid)
Unique Ligands	NA

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4KZD \| pdb_00004kzd	Download File View File

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

(2014) Nat Chem Biol 10: 686-691

Released	2014-06-18
Method	X-RAY DIFFRACTION 2.186 Å
Organisms	Mus musculus
Macromolecule	BL3-6 Fab antibody, heavy chain (protein) BL3-6 Fab antibody, light chain (protein) RNA (84-MER) (nucleic acid)
Unique Ligands	1TU, K, MG
Unique branched monosaccharides	FRU, GLC

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4Q9Q \| pdb_00004q9q	Download File View File

Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab

Huang, H., Suslov, N.B., Li, N.-S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

(2014) Nat Chem Biol 10: 686-691

Released	2014-06-18
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Fab BL3-6, HEAVY CHAIN (protein) Fab BL3-6, LIGHT CHAIN (protein) Spinach RNA aptamer (nucleic acid)
Unique Ligands	2ZZ, K, MG

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4Q9R \| pdb_00004q9r	Download File View File

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

Huang, H., Suslov, N.B., Li, N.-S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

(2014) Nat Chem Biol 10: 686-691

Released	2014-06-18
Method	X-RAY DIFFRACTION 3.12 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Fab BL3-6, HEAVY CHAIN (protein) Fab BL3-6, LIGHT CHAIN (protein) Spinach RNA aptamer (nucleic acid)
Unique Ligands	2ZY, K

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4R4P \| pdb_00004r4p	Download File View File

Crystal Structure of the VS ribozyme-A756G mutant

Piccirilli, J.A., Suslov, N.B., Dasgupta, S., Huang, H., Lilley, D.M.J., Rice, P.A.

(2015) Nat Chem Biol 11: 840-846

Released	2015-09-30
Method	X-RAY DIFFRACTION 3.07 Å
Organisms	Neurospora
Macromolecule	VS ribozyme RNA (nucleic acid)
Unique Ligands	MG

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4R4V \| pdb_00004r4v	Download File View File

Crystal structure of the VS ribozyme - G638A mutant

Piccirilli, J.A., Suslov, N.B., Dasgupta, S., Huang, H., Lilley, D.M.J., Rice, P.A.

(2015) Nat Chem Biol 11: 840-846

Released	2015-09-30
Method	X-RAY DIFFRACTION 3.07 Å
Organisms	Neurospora
Macromolecule	VS ribozyme RNA (nucleic acid)
Unique Ligands	K, MG

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5AOX \| pdb_00005aox	Download File View File

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation

Ahl, V., Weichenrieder, O.

(2015) Mol Cell 60: 715

Released	2015-11-11
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN (protein) SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (protein) ALU JO CONSENSUS RNA (nucleic acid)
Unique Ligands	ACT, MG, PEG, SO4

1 to 25 of 39 Structures

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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

1D4R | pdb_00001d4r

1E8O | pdb_00001e8o

1RY1 | pdb_00001ry1

1Y27 | pdb_00001y27

3DIY | pdb_00003diy

3KTV | pdb_00003ktv

3NCU | pdb_00003ncu

3OWI | pdb_00003owi

3OWW | pdb_00003oww

3OWZ | pdb_00003owz

3OX0 | pdb_00003ox0

3OXB | pdb_00003oxb

3OXD | pdb_00003oxd

3OXE | pdb_00003oxe

3OXJ | pdb_00003oxj

3OXM | pdb_00003oxm

3ZD4 | pdb_00003zd4

3ZD5 | pdb_00003zd5

3ZP8 | pdb_00003zp8

4KZD | pdb_00004kzd

4Q9Q | pdb_00004q9q

4Q9R | pdb_00004q9r

4R4P | pdb_00004r4p

4R4V | pdb_00004r4v

5AOX | pdb_00005aox