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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

QUERY: Structure Author = "Stahl, A."

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This query matches 81 Structures.

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1V9M	Download File View File

Crystal structure of the C subunit of V-type ATPase from Thermus thermophilus

Numoto, N., Kita, A., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Acta Crystallogr D Biol Crystallogr 60: 810-815

Released	2004-05-04
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Thermus thermophilus
Macromolecule	V-type ATP synthase subunit C (protein)
Unique Ligands	GOL

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1WNR	Download File View File

Crystal structure of the Cpn10 from Thermus thermophilus HB8

Numoto, N., Kita, A., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proteins 58: 498-500

Released	2004-12-07
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Thermus thermophilus
Macromolecule	10 kDa chaperonin (protein)

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2D2M	Download File View File

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.

(2005) Proc Natl Acad Sci U S A 102: 14521-14526

Released	2005-10-25
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Oligobrachia mashikoi
Macromolecule	Giant hemoglobin, A1(b) globin chain (protein) Giant hemoglobin, A2(a5) globin chain (protein) Giant hemoglobin, B1(d) globin chain (protein) Giant hemoglobin, B2(c) globin chain (protein)
Unique Ligands	HEM, OXY

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2D2N	Download File View File

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.

(2005) Proc Natl Acad Sci U S A 102: 14521-14526

Released	2005-10-25
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Oligobrachia mashikoi
Macromolecule	Giant hemoglobin, A1(b) globin chain (protein) Giant hemoglobin, A2(a5) globin chain (protein) Giant hemoglobin, B1(d) globin chain (protein) Giant hemoglobin, B2(c) globin chain (protein)
Unique Ligands	HEM, MMC, OXY

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2E0I	Download File View File

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor

Fujihashi, M., Numoto, N., Kobayashi, Y., Mizushima, A., Tsujimura, M., Nakamura, A., Kawarabayashi, Y., Miki, K.

(2007) J Mol Biol 365: 903-910

Released	2006-11-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	432aa long hypothetical deoxyribodipyrimidine photolyase (protein)
Unique Ligands	FAD, MPD

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2ZFO	Download File View File

Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins

Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.

(2008) Proteins 73: 113-125

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Oligobrachia mashikoi
Macromolecule	Extracellular giant hemoglobin major globin subunit A1 (protein) Extracellular giant hemoglobin major globin subunit A2 (protein) Extracellular giant hemoglobin major globin subunit B1 (protein) Extracellular giant hemoglobin major globin subunit B2 (protein)
Unique Ligands	GOL, HEM, OXY

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2ZS0	Download File View File

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin

Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.

(2008) Biochemistry 47: 11231-11238

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Oligobrachia mashikoi
Macromolecule	Extracellular giant hemoglobin major globin subunit A1 (protein) Extracellular giant hemoglobin major globin subunit A2 (protein) Extracellular giant hemoglobin major globin subunit B1 (protein) Extracellular giant hemoglobin major globin subunit B2 (protein)
Unique Ligands	CA, CL, GOL, HEM, OXY

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2ZS1	Download File View File

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin

Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.

(2008) Biochemistry 47: 11231-11238

Released	2008-10-21
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Oligobrachia mashikoi
Macromolecule	Extracellular giant hemoglobin major globin subunit A1 (protein) Extracellular giant hemoglobin major globin subunit A2 (protein) Extracellular giant hemoglobin major globin subunit B1 (protein) Extracellular giant hemoglobin major globin subunit B2 (protein)
Unique Ligands	CL, GOL, HEM, MG, OXY

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3A5C	Download File View File

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

Numoto, N., Hasegawa, Y., Takeda, K., Miki, K.

(2009) EMBO Rep 10: 1228-1234

Released	2009-10-13
Method	X-RAY DIFFRACTION 4.51 Å
Organisms	Thermus thermophilus HB8
Macromolecule	V-type ATP synthase alpha chain (protein) V-type ATP synthase beta chain (protein) V-type ATP synthase subunit D (protein) V-type ATP synthase subunit F (protein)
Unique Ligands	ADP

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3A5D	Download File View File

Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase

Numoto, N., Hasegawa, Y., Takeda, K., Miki, K.

(2009) EMBO Rep 10: 1228-1234

Released	2009-10-13
Method	X-RAY DIFFRACTION 4.8 Å
Organisms	Thermus thermophilus HB8
Macromolecule	V-type ATP synthase alpha chain (protein) V-type ATP synthase beta chain (protein) V-type ATP synthase subunit D (protein) V-type ATP synthase subunit F (protein)

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3W3A	Download File View File

Crystal structure of V1-ATPase at 3.9 angstrom resolution

Nagamatsu, Y., Takeda, K., Kuranaga, T., Numoto, N., Miki, K.

(2013) J Mol Biol 425: 2699-2708

Released	2013-05-15
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Thermus thermophilus HB8
Macromolecule	V-type ATP synthase alpha chain (protein) V-type ATP synthase beta chain (protein) V-type ATP synthase subunit D (protein) V-type ATP synthase subunit F (protein)
Unique Ligands	ADP

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3WCT	Download File View File

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form

Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1823-1831

Released	2014-06-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Lamellibrachia satsuma
Macromolecule	A1 globin chain of giant V2 hemoglobin (protein) A2 globin chain of giant V2 hemoglobin (protein) B1 globin chain of giant V2 hemoglobin (protein) B2 globin chain of giant V2 hemoglobin (protein)
Unique Ligands	CA, HEM, OXY
Unique branched monosaccharides	FUC, MAN, NAG

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3WCU	Download File View File

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Deoxygenated form

Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1823-1831

Released	2014-06-04
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Lamellibrachia satsuma
Macromolecule	A1 globin chain of giant V2 hemoglobin (protein) A2 globin chain of giant V2 hemoglobin (protein) B1 globin chain of giant V2 hemoglobin (protein) B2 globin chain of giant V2 hemoglobin (protein)
Unique Ligands	CA, HEM
Unique branched monosaccharides	FUC, MAN, NAG

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3WCV	Download File View File

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: CA bound form

Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1823-1831

Released	2014-06-04
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Lamellibrachia satsuma
Macromolecule	A1 globin chain of giant V2 hemoglobin (protein) A2 globin chain of giant V2 hemoglobin (protein) B1 globin chain of giant V2 hemoglobin (protein) B2 globin chain of giant V2 hemoglobin (protein)
Unique Ligands	CA, HEM, OXY
Unique branched monosaccharides	FUC, MAN, NAG

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3WCW	Download File View File

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: MG bound form

Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1823-1831

Released	2014-06-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Lamellibrachia satsuma
Macromolecule	A1 globin chain of giant V2 hemoglobin (protein) A2 globin chain of giant V2 hemoglobin (protein) B1 globin chain of giant V2 hemoglobin (protein) B2 globin chain of giant V2 hemoglobin (protein)
Unique Ligands	HEM, MG, OXY
Unique branched monosaccharides	FUC, MAN, NAG

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4X42	Download File View File

Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3

Kulkarni, M.R., Islam, M.M., Numoto, N., Elahi, M.M., Ito, N., Kuroda, Y.

(2015) Biochim Biophys Acta 1854: 1438-1443

Released	2015-09-09
Method	X-RAY DIFFRACTION 2.78 Å
Organisms	Dengue virus 4 Dominica/814669/1981
Macromolecule	Envelope protein E (protein)
Unique Ligands	SO4

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5AUL	Download File View File

PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ikura, T., Oda, M., Ito, N.

(2017) J Biol Chem 292: 1052-1060

Released	2016-05-25
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase regulatory subunit alpha (protein) T-cell-specific surface glycoprotein CD28 (protein)
Unique Ligands	GOL

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5B1C	Download File View File

Crystal structure of DEN4 ED3 mutant with L387I

Kulkarni, M.R., Numoto, N., Ito, N., Kuroda, Y.

(2016) Biochem Biophys Res Commun 471: 163-168

Released	2016-02-24
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Dengue virus 4 Dominica/814669/1981
Macromolecule	Envelope protein E (protein)
Unique Ligands	SO4

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5B1R	Download File View File

Crystal structure of mouse CD72a CTLD

Shinagawa, K., Numoto, N., Tsubata, T., Ito, N.

(2016) J Exp Med 213: 2691-2706

Released	2016-10-19
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Mus musculus
Macromolecule	B-cell differentiation antigen CD72 (protein)
Unique Ligands	ACT, GOL

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5GJH	Download File View File

Gads SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ogawa, S., Ikura, T., Abe, R., Ito, N., Oda, M.

(2017) J Biol Chem 292: 1052-1060

Released	2016-12-14
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Homo sapiens
Macromolecule	GRB2-related adapter protein 2 (protein) T-cell-specific surface glycoprotein CD28 (protein)

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5GJI	Download File View File

PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex

Inaba, S., Numoto, N., Morii, H., Ogawa, S., Ikura, T., Abe, R., Ito, N., Oda, M.

(2017) J Biol Chem 292: 1052-1060

Released	2016-12-14
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase regulatory subunit alpha (protein) T-cell-specific surface glycoprotein CD28 (protein)
Unique Ligands	GOL, SO4

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5XZF	Download File View File

Vitamin D receptor with a synthetic ligand ADRO1

Otero, R., Numoto, N., Ikura, T., Yamada, S., Mourino, A., Makishima, M., Ito, N.

(2018) J Med Chem 61: 6658-6673

Released	2018-07-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	8J0, FMT

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5XZH	Download File View File

Vitamin D receptor with a synthetic ligand ADRO2

Otero, R., Numoto, N., Ikura, T., Yamada, S., Mourino, A., Makishima, M., Ito, N.

(2018) J Med Chem 61: 6658-6673

Released	2018-07-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	8J3

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5ZNO	Download File View File

Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state

Numoto, N., Inaba, S., Yamagami, Y., Kamiya, N., Bekker, G.J., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.

(2018) Biochemistry 57: 5289-5300

Released	2018-09-12
Method	X-RAY DIFFRACTION 1.60264346898 Å
Organisms	Saccharomonospora viridis
Macromolecule	Alpha/beta hydrolase family protein (protein)
Unique Ligands	CA, GOL

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5ZQU	Download File View File

Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN

Miyashita, Y., Numoto, N., Arulmozhiraja, S., Nakano, S., Matsuo, N., Shimizu, K., Kakuta, H., Ito, S., Ikura, T., Ito, N., Tokiwa, H.

(2019) FEBS Lett 593: 242-250

Released	2019-02-27
Method	X-RAY DIFFRACTION 2.60038789589 Å
Organisms	Homo sapiens
Macromolecule	Retinoic acid receptor RXR-alpha (protein)
Unique Ligands	9HF, BR