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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kikuchi, A."

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Search Summary

This query matches 21 Structures.

Refinements

Structure Determination Methodology

experimental (21)

Scientific Name of Source Organism

	Homo sapiens (6)
	Kribbella flavida DSM 17836 (4)
	Lithophyllon concinna (4)
	synthetic construct (4)
	Echinophyllia sp. SC22 (3)
	Rattus norvegicus (2)
	Mus musculus (1)
	Pectiniidae (1)

Taxonomy

	Eukaryota (17)
	Bacteria (4)
	other sequences (4)

Experimental Method

	X-RAY DIFFRACTION (14)
	ELECTRON MICROSCOPY (4)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (21)
	DNA (4)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (8)
	2.0 - 2.5 (4)
	2.5 - 3.0 (2)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (9)
	2020 - 2024 (7)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (4)
	Transferases (3)
	Oxidoreductases (1)

Symmetry Type

	Asymmetric (18)
	Cyclic (2)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (10)
	All alpha proteins (2)
	Artifacts (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 21 of 21 Structures

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1EF5 \| pdb_00001ef5	Download File View File

SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF RGL

Kigawa, T., Endo, M., Ito, Y., Shirouzu, M., Kikuchi, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1998) FEBS Lett 441: 413-418

Released	2000-02-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	RGL (protein)

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1GCU \| pdb_00001gcu	Download File View File

CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A

Kikuchi, A., Park, S.Y., Shiro, Y.

(2001) Nat Struct Biol 8: 221-225

Released	2001-02-08
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Rattus norvegicus
Macromolecule	BILIVERDIN REDUCTASE A (protein)

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1INZ \| pdb_00001inz	Download File View File

SOLUTION STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN OF HUMAN EPSIN

Koshiba, S., Kigawa, T., Kikuchi, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) J Struct Funct Genomics 2: 1-8

Released	2001-05-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	EPS15-INTERACTING PROTEIN(EPSIN) (protein)

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1IQ3 \| pdb_00001iq3	Download File View File

SOLUTION STRUCTURE OF THE EPS15 HOMOLOGY DOMAIN OF A HUMAN POB1

Koshiba, S., Kigawa, T., Iwahara, J., Kikuchi, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1999) FEBS Lett 442: 138-142

Released	2001-06-27
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	RALBP1-INTERACTING PROTEIN (PARTNER OF RALBP1) (protein)
Unique Ligands	CA

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1WSP \| pdb_00001wsp	Download File View File

Crystal structure of axin dix domain

Shibata, N., Hanamura, T., Yamamoto, R., Ueda, Y., Yamamoto, H., Kikuchi, A., Higuchi, Y.

To be published

Released	2006-02-14
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Rattus norvegicus
Macromolecule	Axin 1 protein (protein)
Unique Ligands	BEZ, HG

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2Z1O \| pdb_00002z1o	Download File View File

Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state

Kikuchi, A., Jeyakanthan, J., Taka, J., Shiro, Y., Mizuno, H., Miyawaki, A.

(2008) Proc Natl Acad Sci U S A 105: 9227-9232

Released	2008-05-13
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Echinophyllia sp. SC22
Macromolecule	Fluorescent protein Dronpa (protein)

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2Z6X \| pdb_00002z6x	Download File View File

Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein Dronpa

Kikuchi, A., Jeyakanthan, J., Taka, J., Shiro, Y., Mizuno, H., Miyawaki, A.

(2008) Proc Natl Acad Sci U S A 105: 9227-9232

Released	2008-07-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pectiniidae
Macromolecule	photochromic protein Dronpa (protein)

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2Z6Y \| pdb_00002z6y	Download File View File

Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state

Kikuchi, A., Jeyakanthan, J., Taka, J., Shiro, Y., Mizuno, H., Miyawaki, A.

(2008) Proc Natl Acad Sci U S A 105: 9227-9232

Released	2008-07-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Echinophyllia sp. SC22
Macromolecule	Fluorescent protein Dronpa (protein)

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2Z6Z \| pdb_00002z6z	Download File View File

Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state

Kikuchi, A., Jeyakanthan, J., Taka, J., Shiro, Y., Mizuno, H., Miyawaki, A.

(2008) Proc Natl Acad Sci U S A 105: 9227-9232

Released	2008-07-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Echinophyllia sp. SC22
Macromolecule	Fluorescent protein Dronpa (protein)

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2ZMU \| pdb_00002zmu	Download File View File

Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 9.1

Kikuchi, A., Fukumura, E., Karasawa, S., Mizuno, H., Miyawaki, A., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Biochemistry 47: 11573-11580

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Lithophyllon concinna
Macromolecule	Fluorescent protein (protein)

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2ZMW \| pdb_00002zmw	Download File View File

Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 6.0

Kikuchi, A., Fukumura, E., Karasawa, S., Mizuno, H., Miyawaki, A., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Biochemistry 47: 11573-11580

Released	2008-10-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Lithophyllon concinna
Macromolecule	Fluorescent protein (protein)

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2ZO6 \| pdb_00002zo6	Download File View File

Crystal Structure of Kusabira-Cyan (KCY), a Cyan-Emitting GFP-Like Protein

Kikuchi, A., Fukumura, E., Karasawa, S., Miyawaki, A., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Biochemistry 48: 5276-5283

Released	2009-05-12
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Lithophyllon concinna
Macromolecule	CYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY) (protein)

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2ZO7 \| pdb_00002zo7	Download File View File

Crystal Structure of a Kusabira-Cyan Mutant (KCY-R1), a Cyan/Green-Emitting GFP-Like Protein

Kikuchi, A., Fukumura, E., Karasawa, S., Miyawaki, A., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Biochemistry 48: 5276-5283

Released	2009-05-12
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Lithophyllon concinna
Macromolecule	CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1) (protein)

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7C24 \| pdb_00007c24	Download File View File

Glycosidase F290Y at pH8.0

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	GOL, NH4

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7C25 \| pdb_00007c25	Download File View File

Glycosidase Wild Type at pH8.0

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.505 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

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7C26 \| pdb_00007c26	Download File View File

Glycosidase Wild Type at pH4.5

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.803 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

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7C27 \| pdb_00007c27	Download File View File

Glycosidase F290Y at pH4.5

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

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7XI9 \| pdb_00007xi9	Download File View File

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)

Onoda, H., Kikuchi, A., Kori, S., Yoshimi, S., Yamagata, A., Arita, K.

(2022) Nat Commun 13: 7130-7130

Released	2022-11-30
Method	ELECTRON MICROSCOPY 2.52 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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7XIB \| pdb_00007xib	Download File View File

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)

Onoda, H., Kikuchi, A., Kori, S., Yoshimi, S., Yamagata, A., Arita, K.

(2022) Nat Commun 13: 7130-7130

Released	2022-11-30
Method	ELECTRON MICROSCOPY 2.23 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	ZN

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8XQC \| pdb_00008xqc	Download File View File

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

Kikuchi, A., Hayashi, G., Kori, S., Arita, K.

To be published

Released	2025-01-15
Method	ELECTRON MICROSCOPY 3.25 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') (nucleic acid) DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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8YV8 \| pdb_00008yv8	Download File View File

Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence.

Kikuchi, A., Shikimachi, R., Nishiyama, A., Funabiki, H., Arita, K.

(2024) Sci Adv 10: eadp5753-eadp5753

Released	2024-07-31
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	ZN

1 to 21 of 21 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

1EF5 | pdb_00001ef5

1GCU | pdb_00001gcu

1INZ | pdb_00001inz

1IQ3 | pdb_00001iq3

1WSP | pdb_00001wsp

2Z1O | pdb_00002z1o

2Z6X | pdb_00002z6x

2Z6Y | pdb_00002z6y

2Z6Z | pdb_00002z6z

2ZMU | pdb_00002zmu

2ZMW | pdb_00002zmw

2ZO6 | pdb_00002zo6

2ZO7 | pdb_00002zo7

7C24 | pdb_00007c24

7C25 | pdb_00007c25

7C26 | pdb_00007c26

7C27 | pdb_00007c27

7XI9 | pdb_00007xi9

7XIB | pdb_00007xib

8XQC | pdb_00008xqc

8YV8 | pdb_00008yv8