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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "TRANSFERASE/RNA"

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Search Summary

This query matches 283 Structures.

Refinements

Structure Determination Methodology

experimental (283)

Scientific Name of Source Organism

	synthetic construct (70)
	Homo sapiens (38)
	Archaeoglobus fulgidus (26)
	Thermotoga maritima MSB8 (17)
	Aquifex aeolicus VF5 (14)
	Enterovirus A71 (13)
	Hepatitis C virus JFH-1 (13)
	Saccharomyces cerevisiae (13)
	Escherichia coli (9)
	Escherichia coli O157:H7 (9)

More...

Taxonomy

	Riboviria (98)
	Eukaryota (75)
	Bacteria (72)
	other sequences (70)
	Archaea (49)
	Duplodnaviria (2)
	Varidnaviria (2)

Experimental Method

	X-RAY DIFFRACTION (247)
	ELECTRON MICROSCOPY (35)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (283)
	RNA (269)
	DNA (20)
	NA-hybrid (10)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (21)
	2.0 - 2.5 (41)
	2.5 - 3.0 (113)
	3.0 - 3.5 (62)
	3.5 - 4.0 (26)
	4.0 - 4.5 (9)
	> 4.5 (8)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (12)
	2005 - 2009 (60)
	2010 - 2014 (70)
	2015 - 2019 (87)
	2020 - 2024 (52)

Enzyme Classification Name

	Transferases (265)
	Hydrolases (14)
	Ligases (1)

Symmetry Type

	Asymmetric (235)
	Cyclic (46)
	Dihedral (8)
	Helical (1)

SCOP Classification

	Multi-domain proteins (alpha and beta) (43)
	Alpha and beta proteins (a+b) (30)
	All alpha proteins (31)
	Artifacts (21)
	Alpha and beta proteins (a/b) (14)
	Low resolution protein structures (3)
	All beta proteins (4)
	Small proteins (3)
	Peptides (1)

AllSelected

1 to 25 of 283 Structures

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1AV6 \| pdb_00001av6	Download File View File

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE

Hodel, A.E., Gershon, P.D., Quiocho, F.A.

(1998) Mol Cell 1: 443-447

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Vaccinia virus WR
Macromolecule	Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (protein) RNA (5'-R(GPAPAPAPAPA)-3') (nucleic acid)
Unique Ligands	MGT, SAH

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1HVU \| pdb_00001hvu	Download File View File

HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE COMPLEXED WITH A 33-BASE NUCLEOTIDE RNA PSEUDOKNOT

Jaeger, J., Restle, T., Steitz, T.A.

(1998) EMBO J 17: 4535-4542

Released	1999-01-13
Method	X-RAY DIFFRACTION 4.75 Å
Organisms	Human immunodeficiency virus 1
Macromolecule	PROTEIN (HIV-1 REVERSE TRANSCRIPTASE) (protein) RNA (33 NUCLEOTIDE RNA PSEUDOKNOT) (nucleic acid)

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1J2B \| pdb_00001j2b	Download File View File

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)

Ishitani, R., Nureki, O., Nameki, N., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Cell 113: 383-394

Released	2003-05-27
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Pyrococcus horikoshii
Macromolecule	Archaeosine tRNA-guanine transglycosylase (protein) tRNA(Val) (nucleic acid)
Unique Ligands	MG, ZN

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1N1H \| pdb_00001n1h	Download File View File

Initiation complex of polymerase lambda3 from reovirus

Tao, Y., Farsetta, D.L., Nibert, M.L., Harrison, S.C.

(2002) Cell 111: 733-745

Released	2002-12-25
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mammalian orthoreovirus 3 Dearing
Macromolecule	Minor core protein lambda 3 (protein) 5'-R(APUPUPAPGPC)-3' (nucleic acid)
Unique Ligands	CH1, G7M, GDP, GH3, MN

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1N35 \| pdb_00001n35	Download File View File

lambda3 elongation complex with four phosphodiester bond formed

Tao, Y., Farsetta, D.L., Nibert, M.L., Harrison, S.C.

(2002) Cell 111: 733-745

Released	2002-12-25
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mammalian orthoreovirus 3 Dearing
Macromolecule	Minor core protein lambda 3 (protein) 5'-R(APUPUPAPGPCPCPCPCPC)-3' (nucleic acid) 5'-R(PGPGPGPGP*G)-3' (nucleic acid)
Unique Ligands	CH1, MN

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1N38 \| pdb_00001n38	Download File View File

reovirus polymerase lambda3 elongation complex with one phosphodiester bond formed

Tao, Y., Farsetta, D.L., Nibert, M.L., Harrison, S.C.

(2002) Cell 111: 733-745

Released	2002-12-25
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mammalian orthoreovirus 3 Dearing
Macromolecule	Minor core protein lambda 3 (protein) 5'-R(APUPUPAPGPC)-3' (nucleic acid) 5'-R(PGPC)-3' (nucleic acid)
Unique Ligands	CH1, MN, U3H

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1NB7 \| pdb_00001nb7	Download File View File

HC-J4 RNA polymerase complexed with short RNA template strand

O'Farrell, D.J., Trowbridge, R., Rowlands, D.J., Jaeger, J.

(2003) J Mol Biology 326: 1025-1035

Released	2003-03-25
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Hepacivirus hominis
Macromolecule	polyprotein (protein) 5'-R(UPUPUPU)-3' (nucleic acid)
Unique Ligands	MN

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1Q2R \| pdb_00001q2r	Download File View File

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Xie, W., Liu, X., Huang, R.H.

(2003) Nat Struct Biol 10: 781-788

Released	2003-09-09
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Zymomonas mobilis synthetic construct
Macromolecule	Queuine tRNA-ribosyltransferase (protein) RNA (5'-R(APGPCPAPCPGPGPCPUP(N)PUPAPAPAPCPCPGPUPGPC)-3') (nucleic acid)
Unique Ligands	9DG, ZN

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1Q2S \| pdb_00001q2s	Download File View File

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Xie, W., Liu, X., Huang, R.H.

(2003) Nat Struct Biol 10: 781-788

Released	2003-09-09
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Zymomonas mobilis synthetic construct
Macromolecule	Queuine tRNA-ribosyltransferase (protein) 5'-R(APGPCPAPCPGPGPCPUP(PQ1)PUPAPAPAPCPCPGPUPGPC)-3' (nucleic acid) RNA (5'-R(APGPCPAPCPGPGPCPUP(N)PUPAPAPAPCPCPGPUPGPC)-3') (nucleic acid)
Unique Ligands	9DG, ZN

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1SZ1 \| pdb_00001sz1	Download File View File

Mechanism of CCA-adding enzymes specificity revealed by crystal structures of ternary complexes

Xiong, Y., Steitz, T.A.

(2004) Nature 430: 640-645

Released	2004-08-10
Method	X-RAY DIFFRACTION 6.21 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	tRNA nucleotidyltransferase (protein) T-RNA (76-MER) (nucleic acid)

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1TFW \| pdb_00001tfw	Download File View File

How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template

Xiong, Y., Steitz, T.A.

(2004) Nature 430: 640-645

Released	2004-08-10
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	tRNA nucleotidyltransferase (protein) 5'-R(CPGPCPGPGPAPUPCPCPGPCPAPC)-3' (nucleic acid) 5'-R(GPCPGPGPAPCPCPCPGPCPAPC)-3' (nucleic acid) 5'-R(GPCPGPGPAPUPCPCPGPCPAPC)-3' (nucleic acid) 5'-R(GPCPGPGPAPUPCPCPGPCPAPCPC)-3' (nucleic acid)
Unique Ligands	ATP, MG

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1TFY \| pdb_00001tfy	Download File View File

How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template

Xiong, Y., Steitz, T.A.

(2004) Nature 430: 640-645

Released	2004-08-10
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	tRNA nucleotidyltransferase (protein) 5'-R(CPGPCPGPGPAPUPC)-3' (nucleic acid) 5'-R(CPGPGPAPUPCPCPGPCPAPC)-3' (nucleic acid) 5'-R(GPCPGPGPAPUPAPUPCPCPGPCPAPC)-3' (nucleic acid) 5'-R(GPCPGPGPAPUPAPUPCPCPGPCPG)-3' (nucleic acid)
Unique Ligands	CTP, MG

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1VFG \| pdb_00001vfg	Download File View File

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog

Tomita, K., Fukai, S., Ishitani, R., Ueda, T., Takeuchi, N., Vassylyev, D.G., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Nature 430: 700-704

Released	2004-08-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Aquifex aeolicus
Macromolecule	poly A polymerase (protein) RNA (75-MER) (nucleic acid)
Unique Ligands	APC

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1WNE \| pdb_00001wne	Download File View File

Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with a template-primer RNA

Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

(2004) J Biological Chem 279: 47212-47221

Released	2004-08-31
Method	X-RAY DIFFRACTION 3 Å
Organisms	Foot-and-mouth disease virus C-S8c1
Macromolecule	RNA-dependent RNA polymerase (protein) 5'-R(CPAPUPGPGPGPCPC)-3' (nucleic acid) 5'-R(GPGPCPCP*C)-3' (nucleic acid)
Unique Ligands	MG

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2B63 \| pdb_00002b63	Download File View File

Complete RNA Polymerase II-RNA inhibitor complex

Kettenberger, H., Eisenfuehr, A., Brueckner, F., Theis, M., Famulok, M., Cramer, P.

(2006) Nat Struct Mol Biol 13: 44-48

Released	2005-12-06
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 12 Unique nucleic acid chains: 1
Unique Ligands	MG, ZN

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2DER \| pdb_00002der	Download File View File

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state

Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

(2006) Nature 442: 419-424

Released	2006-08-15
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Escherichia coli
Macromolecule	tRNA-specific 2-thiouridylase mnmA (protein) tRNA (nucleic acid)
Unique Ligands	PO4, SO4

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2DET \| pdb_00002det	Download File View File

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state

Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

(2006) Nature 442: 419-424

Released	2006-08-15
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Escherichia coli
Macromolecule	tRNA-specific 2-thiouridylase mnmA (protein) tRNA (nucleic acid)
Unique Ligands	SO4

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2DEU \| pdb_00002deu	Download File View File

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated intermediate state

Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., Nureki, O.

(2006) Nature 442: 419-424

Released	2006-08-15
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Escherichia coli
Macromolecule	tRNA-specific 2-thiouridylase mnmA (protein) tRNA (nucleic acid)
Unique Ligands	AMP, SO4

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2DR5 \| pdb_00002dr5	Download File View File

Complex structure of CCA adding enzyme with mini-helix lacking CCA

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-10-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (32-MER) (nucleic acid)
Unique Ligands	SO4

Explore in 3D

2DR7 \| pdb_00002dr7	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDC

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (33-MER) (nucleic acid)
Unique Ligands	SO4

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2DR8 \| pdb_00002dr8	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDC and CTP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (33-MER) (nucleic acid)
Unique Ligands	CTP, MG, SO4

Explore in 3D

2DR9 \| pdb_00002dr9	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDCC

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	SO4

Explore in 3D

2DRA \| pdb_00002dra	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	ATP, MG, SO4

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2DRB \| pdb_00002drb	Download File View File

Complex structure of CCA-adding enzyme with tRNAminiCCA

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (35-MER) (nucleic acid)
Unique Ligands	SO4

Explore in 3D

2DVI \| pdb_00002dvi	Download File View File

Complex structure of CCA-adding enzyme, mini-DCC and CTP

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

Released	2006-11-14
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	CCA-adding enzyme (protein) tRNA (34-MER) (nucleic acid)
Unique Ligands	CTP, MG, SO4

1 to 25 of 283 Structures

Page 1 of 12

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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

1AV6 | pdb_00001av6

1HVU | pdb_00001hvu

1J2B | pdb_00001j2b

1N1H | pdb_00001n1h

1N35 | pdb_00001n35

1N38 | pdb_00001n38

1NB7 | pdb_00001nb7

1Q2R | pdb_00001q2r

1Q2S | pdb_00001q2s

1SZ1 | pdb_00001sz1

1TFW | pdb_00001tfw

1TFY | pdb_00001tfy

1VFG | pdb_00001vfg

1WNE | pdb_00001wne

2B63 | pdb_00002b63

2DER | pdb_00002der

2DET | pdb_00002det

2DEU | pdb_00002deu

2DR5 | pdb_00002dr5

2DR7 | pdb_00002dr7

2DR8 | pdb_00002dr8

2DR9 | pdb_00002dr9

2DRA | pdb_00002dra

2DRB | pdb_00002drb

2DVI | pdb_00002dvi