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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ishibe-Murakami, S."

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Malacoplasma penetrans HF-2 (4)
	synthetic construct (4)
	Mus musculus (3)
	[Eubacterium] siraeum V10Sc8a (3)
	Homo sapiens (1)
	Spodoptera frugiperda (1)

Taxonomy

	Bacteria (7)
	Eukaryota (4)
	other sequences (4)

Experimental Method

X-RAY DIFFRACTION (11)

Polymer Entity Type

	Protein (8)
	DNA (5)
	RNA (4)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (2)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (7)
	2020 - 2024 (4)

Enzyme Classification Name

Transferases (5)

Symmetry Type

Asymmetric (8)

SCOP Classification

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

AllSelected

1 to 11 of 11 Structures

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3SUH \| pdb_00003suh	Download File View File

Crystal structure of THF riboswitch, bound with 5-formyl-THF

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

(2011) Proc Natl Acad Sci U S A 108: 14801-14806

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	[Eubacterium] siraeum V10Sc8a
Macromolecule	Riboswitch (nucleic acid)
Unique Ligands	FFO, NA

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3SUX \| pdb_00003sux	Download File View File

Crystal structure of THF riboswitch, bound with THF

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

(2011) Proc Natl Acad Sci U S A 108: 14801-14806

Released	2011-09-14
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	[Eubacterium] siraeum V10Sc8a
Macromolecule	Riboswitch (nucleic acid)
Unique Ligands	NA, THF

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3SUY \| pdb_00003suy	Download File View File

Crystal structure of THF riboswitch, unbound status

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

(2011) Proc Natl Acad Sci U S A 108: 14801-14806

Released	2011-09-14
Method	X-RAY DIFFRACTION 3.21 Å
Organisms	[Eubacterium] siraeum V10Sc8a
Macromolecule	riboswitch (nucleic acid)

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4DA4 \| pdb_00004da4	Download File View File

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

Song, J., Patel, D.J.

(2012) Science 335: 709-712

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA_LOWER_STRAND (nucleic acid) DNA_UPPER_STRAND (nucleic acid)
Unique Ligands	CIT, SAH, ZN

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4DOV \| pdb_00004dov	Download File View File

Structure of free mouse ORC1 BAH domain

Song, J., Patel, D.J.

(2012) Nature 484: 115-119

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.696 Å
Organisms	Mus musculus
Macromolecule	Origin recognition complex subunit 1 (protein)

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4DOW \| pdb_00004dow	Download File View File

Structure of mouse ORC1 BAH domain bound to H4K20me2

Song, J., Patel, D.J.

(2012) Nature 484: 115-119

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Mus musculus
Macromolecule	Histone H4 (protein) Origin recognition complex subunit 1 (protein)

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4KXT \| pdb_00004kxt	Download File View File

Structure of human ARGONAUTE1 in complex with guide RNA

Nakanishi, K., Patel, D.J.

(2013) Cell Rep 3: 1893-1900

Released	2013-07-31
Method	X-RAY DIFFRACTION 2.294 Å
Organisms	Homo sapiens Spodoptera frugiperda
Macromolecule	Protein argonaute-1 (protein) RNA (nucleic acid)

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8C56 \| pdb_00008c56	Download File View File

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA

Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

(2024) Nucleic Acids Res 52: 9267-9281

Released	2024-01-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Malacoplasma penetrans HF-2 synthetic construct
Macromolecule	Cytosine-specific methyltransferase (protein) DNA (5'-D(CPCPAPCPAPTPGP(5PY)PGPCPTPGPAPA)-3') (nucleic acid) DNA (5'-D(GPTPTPCPAPGP(5CM)PGPCPAPTPGPTPG)-3') (nucleic acid)
Unique Ligands	GOL, NA, SAH

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8C57 \| pdb_00008c57	Download File View File

CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) and 5-methylcytosine containing dsDNA

Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

(2024) Nucleic Acids Res 52: 9267-9281

Released	2024-01-17
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Malacoplasma penetrans HF-2 synthetic construct
Macromolecule	Cytosine-specific methyltransferase (protein) DNA (5'-D(CPCPAPCPAPTPGP(5MA)PGPCPTPGPAPA)-3') (nucleic acid) DNA (5'-D(GPTPTPCPAPGP(5CM)PGPCPAPTPGPTPG)-3') (nucleic acid)
Unique Ligands	CO3, GOL, SAM

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8C58 \| pdb_00008c58	Download File View File

CpG specific M.MpeI methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA

Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

(2024) Nucleic Acids Res 52: 9267-9281

Released	2024-01-17
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Malacoplasma penetrans HF-2 synthetic construct
Macromolecule	Cytosine-specific methyltransferase (protein) DNA (5'-D(CPCPAPCPAPTPGP(5OC)PGPCPTPGPAPA)-3') (nucleic acid) DNA (5'-D(GPTPTPCPAPGP(5CM)PGPCPAPTPGPTPG)-3') (nucleic acid)
Unique Ligands	CO3, GOL, SAM

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8C59 \| pdb_00008c59	Download File View File

CpG specific M.MpeI methyltransferase crystallized in the presence of 5-bromocytosine (converted to 5mC) and 5-methylcytosine containing dsDNA

Wojciechowski, M., Czapinska, H., Krwawicz, J., Rafalski, D., Bochtler, M.

(2024) Nucleic Acids Res 52: 9267-9281

Released	2024-01-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Malacoplasma penetrans HF-2 synthetic construct
Macromolecule	Cytosine-specific methyltransferase (protein) DNA (5'-D(CPCPAPCPAPTPGP(5CM)PGPCPTPGPAPA)-3') (nucleic acid) DNA (5'-D(GPTPTPCPAPGP(5CM)PGPCPAPTPGPTPG)-3') (nucleic acid)
Unique Ligands	CIT, CO3, GOL, NA, SAM

1 to 11 of 11 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.

3SUH | pdb_00003suh

Crystal structure of THF riboswitch, bound with 5-formyl-THF

3SUX | pdb_00003sux

Crystal structure of THF riboswitch, bound with THF

3SUY | pdb_00003suy

Crystal structure of THF riboswitch, unbound status

4DA4 | pdb_00004da4

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

4DOV | pdb_00004dov

Structure of free mouse ORC1 BAH domain

4DOW | pdb_00004dow

Structure of mouse ORC1 BAH domain bound to H4K20me2

4KXT | pdb_00004kxt

Structure of human ARGONAUTE1 in complex with guide RNA

8C56 | pdb_00008c56

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA

8C57 | pdb_00008c57

CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) and 5-methylcytosine containing dsDNA

8C58 | pdb_00008c58

CpG specific M.MpeI methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA

8C59 | pdb_00008c59

CpG specific M.MpeI methyltransferase crystallized in the presence of 5-bromocytosine (converted to 5mC) and 5-methylcytosine containing dsDNA

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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

3SUH | pdb_00003suh

3SUX | pdb_00003sux

3SUY | pdb_00003suy

4DA4 | pdb_00004da4

4DOV | pdb_00004dov

4DOW | pdb_00004dow

4KXT | pdb_00004kxt

8C56 | pdb_00008c56

8C57 | pdb_00008c57

8C58 | pdb_00008c58

8C59 | pdb_00008c59