RCSB PDB: Search

1DXA \| pdb_00001dxa	Download File View File

BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

Yeh, H.J.C., Sayer, J.M., Liu, X., Altieri, A.S., Byrd, R.A., Lakshman, M.K., Yagi, H., Schurter, E.J., Gorenstein, D.G., Jerina, D.M.

(1995) Biochemistry 34: 13570-13581

Released	1995-12-07
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPTPCPGPGPGPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPCPAPCPGPAPG)-3') (nucleic acid)
Unique Ligands	BAP

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1N8C \| pdb_00001n8c	Download File View File

Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex

Volk, D.E., Thiviyanathan, V., Rice, J.S., Luxon, B.A., Shah, J.H., Yagi, H., Sayer, J.M., Yeh, H.J.C., Jerina, D.M., Gorenstein, D.G.

(2003) Biochemistry 42: 1410-1420

Released	2003-02-14
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPTPCPGPTPGPAPCPCPG)-3' (nucleic acid) 5'-D(CPGPGPTPCPAPCPGPAPGPG)-3' (nucleic acid)
Unique Ligands	TBC

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1WDI \| pdb_00001wdi	Download File View File

Crystal Structure Of TT0907 From Thermus Thermophilus HB8

Idaka, M., Yagi, H., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus
Macromolecule	hypothetical protein TT0907 (protein)
Unique Ligands	CIT

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2E5T \| pdb_00002e5t	Download File View File

C-terminal domain of Epsilon subunit of F1F0-ATP synthase from the Thermophilic bacillus PS3 in the presence of ATP condition

Yagi, H., Akutsu, H.

(2007) Proc Natl Acad Sci U S A 104: 11233-11238

Released	2007-07-10
Method	SOLUTION NMR
Organisms	Bacillus sp. PS3
Macromolecule	ATP synthase epsilon chain (protein)

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2E5U \| pdb_00002e5u	Download File View File

C-terminal domain of Epsilon subunit of F1F0-ATP synthase from the Thermophilic Bacillus PS3

Yagi, H., Akutsu, H.

(2007) Proc Natl Acad Sci U S A 104: 11233-11238

Released	2007-07-10
Method	SOLUTION NMR
Organisms	Bacillus sp. PS3
Macromolecule	ATP synthase epsilon chain (protein)

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2E5Y \| pdb_00002e5y	Download File View File

Epsilon subunit and ATP complex of F1F0-ATP synthase from the Thermophilic Bacillus PS3

Yagi, H., Akutsu, H.

(2007) Proc Natl Acad Sci U S A 104: 11233-11238

Released	2007-07-10
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Bacillus sp. PS3
Macromolecule	ATP synthase epsilon chain (protein)
Unique Ligands	ATP

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2IA6 \| pdb_00002ia6	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPA)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	ATP, BAP, CA, EDO, GOL, PO4

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2IBK \| pdb_00002ibk	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPAPT)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	BAP, CA, EDO, GOL, POP

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2JZ4 \| pdb_00002jz4	Download File View File

Putative 32 kDa myrosinase binding protein At3g16450.1 from Arabidopsis thaliana

Takeda, N., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A.M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Guntert, P., Aceti, D.J., Markley, J.L., Kainosho, M., Center for Eukaryotic Structural Genomics (CESG)

(2008) FEBS J 275: 5873-5884

Released	2008-02-19
Method	SOLUTION NMR
Organisms	Arabidopsis thaliana
Macromolecule	Jasmonate inducible protein isolog (protein)

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2M66 \| pdb_00002m66	Download File View File

Endoplasmic reticulum protein 29 (ERp29) C-terminal domain: 3D Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

Yagi, H., Pilla, K., Maleckis, A., Graham, B., Huber, T., Otting, G.

(2013) Structure 21: 883-890

Released	2013-07-10
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	Endoplasmic reticulum resident protein 29 (protein)

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2ROU \| pdb_00002rou	Download File View File

Stereospecific Conformations of N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adducts: 3'-Intercalation of the 1R Adduct and 5'-Minor Groove Orientation of the 1S Adduct in an Iterated (CG)3 Repeat

Wang, Y., Kroth, H., Yagi, H., Sayer, J.M., Kumar, S., Jerina, D.M., Stone, M.P.

(2008) Chem Res Toxicol 21: 1348-1358

Released	2009-03-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(DAPDTPDCPDGPDCPDGPDCPDGPDGPDCPDAPDTPDG)-3') (nucleic acid) DNA (5'-D(DCPDAPDTPDGPDCPDCPDGPDCPDGPDCPDGPDAPDT)-3') (nucleic acid)
Unique Ligands	BPJ

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2RQ6 \| pdb_00002rq6	Download File View File

Solution structure of the epsilon subunit of the F1-atpase from thermosynechococcus elongatus BP-1

Yagi, H., Konno, H., Murakami-Fuse, T., Oroguchi, H., Akutsu, T., Ikeguchi, M., Hisabori, T.

(2010) Biochem J 425: 85-94

Released	2010-01-12
Method	SOLUTION NMR
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	ATP synthase epsilon chain (protein)

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2RQ7 \| pdb_00002rq7	Download File View File

Solution structure of the epsilon subunit chimera combining the N-terminal beta-sandwich domain from T. Elongatus bp-1 f1 and the C-terminal alpha-helical domain from spinach chloroplast F1

Yagi, H., Konno, H., Murakami-Fuse, T., Oroguchi, H., Akutsu, T., Ikeguchi, M., Hisabori, T.

(2010) Biochem J 425: 85-94

Released	2010-01-12
Method	SOLUTION NMR
Organisms	Spinacia oleracea Thermosynechococcus vestitus BP-1
Macromolecule	ATP synthase epsilon chain,ATP synthase epsilon chain, chloroplastic (protein)

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3AY4 \| pdb_00003ay4	Download File View File

Crystal structure of nonfucosylated Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Mizushima, T., Takemoto, E., Yagi, H., Shibata-Koyama, M., Isoda, Y., Iida, S., Satoh, M., Kato, K.

(2011) Genes Cells 16: 1071-1080

Released	2011-08-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Ig gamma-1 chain C region (protein) Low affinity immunoglobulin gamma Fc region receptor III-A (protein)
Unique branched monosaccharides	BMA, FUC, GAL, MAN, NAG

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3VR0 \| pdb_00003vr0	Download File View File

Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator

Kumoi, K., Satoh, T., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Murata, K., Yagi, H., Kato, K.

(2013) PLoS One 8: e60294-e60294

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	AU

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3WHJ \| pdb_00003whj	Download File View File

Crystal structure of Nas2 N-terminal domain

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein)
Unique Ligands	CD, SO4

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3WHK \| pdb_00003whk	Download File View File

Crystal structure of PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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3WHL \| pdb_00003whl	Download File View File

Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 4 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein) Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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4DBG \| pdb_00004dbg	Download File View File

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative

Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.

(2012) EMBO Rep 13: 462-468

Released	2012-04-04
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Homo sapiens
Macromolecule	RING finger protein 31 (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)

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4Y1S \| pdb_00004y1s	Download File View File

Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes

Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.

(2015) J Biological Chem 290: 25213-25226

Released	2015-09-02
Method	X-RAY DIFFRACTION 1.611 Å
Organisms	Mus musculus
Macromolecule	Perforin-1 (protein)
Unique Ligands	CA

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4Y1T \| pdb_00004y1t	Download File View File

Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes

Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.

(2015) J Biological Chem 290: 25213-25226

Released	2015-09-02
Method	X-RAY DIFFRACTION 2.666 Å
Organisms	Mus musculus
Macromolecule	Perforin-1 (protein)
Unique Ligands	CA

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5BW7 \| pdb_00005bw7	Download File View File

Crystal structure of nonfucosylated Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Isoda, Y., Yagi, H., Satoh, T., Shibata-Koyama, M., Masuda, K., Satoh, M., Kato, K., Iida, S.

(2015) PLoS One 10: e0140120-e0140120

Released	2015-10-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Ig gamma-1 chain C region (protein) Low affinity immunoglobulin gamma Fc region receptor III-A (protein)
Unique Ligands	CL
Unique branched monosaccharides	BMA, FUC, GAL, MAN, NAG

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5XJE \| pdb_00005xje	Download File View File

Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Sakae, Y., Satoh, T., Yagi, H., Yanaka, S., Yamaguchi, T., Isoda, Y., Iida, S., Okamoto, Y., Kato, K.

(2017) Sci Rep 7: 13780-13780

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Immunoglobulin gamma-1 heavy chain (protein) Low affinity immunoglobulin gamma Fc region receptor III-A (protein)
Unique Ligands	CL
Unique branched monosaccharides	BMA, FUC, GAL, MAN, NAG

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5XJF \| pdb_00005xjf	Download File View File

Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Sakae, Y., Satoh, T., Yagi, H., Yanaka, S., Yamaguchi, T., Isoda, Y., Iida, S., Okamoto, Y., Kato, K.

(2017) Sci Rep 7: 13780-13780

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Immunoglobulin gamma-1 heavy chain (protein) Low affinity immunoglobulin gamma Fc region receptor III-A (protein)
Unique Ligands	CL, NAG
Unique branched monosaccharides	BMA, FUC, GAL, MAN, NAG

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6KRU \| pdb_00006kru	Download File View File

Crystal structure of mouse IgG2b Fc

Taniguchi, Y., Satoh, T., Yagi, H., Kato, K.

(2019) Int J Mol Sci 21:

Released	2020-01-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Mus musculus
Macromolecule	Ig gamma-2B chain C region (protein)
Unique branched monosaccharides	FUC, GAL, MAN, NAG

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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

1DXA | pdb_00001dxa

1N8C | pdb_00001n8c

1WDI | pdb_00001wdi

2E5T | pdb_00002e5t

2E5U | pdb_00002e5u

2E5Y | pdb_00002e5y

2IA6 | pdb_00002ia6

2IBK | pdb_00002ibk

2JZ4 | pdb_00002jz4

2M66 | pdb_00002m66

2ROU | pdb_00002rou

2RQ6 | pdb_00002rq6

2RQ7 | pdb_00002rq7

3AY4 | pdb_00003ay4

3VR0 | pdb_00003vr0

3WHJ | pdb_00003whj

3WHK | pdb_00003whk

3WHL | pdb_00003whl

4DBG | pdb_00004dbg

4Y1S | pdb_00004y1s

4Y1T | pdb_00004y1t

5BW7 | pdb_00005bw7

5XJE | pdb_00005xje

5XJF | pdb_00005xjf

6KRU | pdb_00006kru