RCSB PDB: Search

1IU1 \| pdb_00001iu1	Download File View File

Crystal structure of human gamma1-adaptin ear domain

Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K., Wakatsuki, S.

(2002) Nat Struct Biol 9: 527-531

Released	2002-07-10
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	gamma1-adaptin (protein)

Explore in 3D

1J2J \| pdb_00001j2j	Download File View File

Crystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	ADP-ribosylation factor 1 (protein) ADP-ribosylation factor binding protein GGA1 (protein)
Unique Ligands	GTP, IOD, MG

Explore in 3D

1JWF \| pdb_00001jwf	Download File View File

Crystal Structure of human GGA1 VHS domain.

Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

(2002) Nature 415: 937-941

Released	2002-03-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein)

Explore in 3D

1JWG \| pdb_00001jwg	Download File View File

VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide

Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K., Wakatsuki, S.

(2002) Nature 415: 937-941

Released	2002-03-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein) Cation-independent mannose-6-phosphate receptor (protein)
Unique Ligands	IOD

Explore in 3D

1O3X \| pdb_00001o3x	Download File View File

Crystal structure of human GGA1 GAT domain

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA1 (protein)

Explore in 3D

1O3Y \| pdb_00001o3y	Download File View File

Crystal structure of mouse ARF1 (delta17-Q71L), GTP form

Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2003) Nat Struct Biol 10: 386-393

Released	2003-05-20
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mus musculus
Macromolecule	ADP-ribosylation factor 1 (protein)
Unique Ligands	GTP, MG

Explore in 3D

1WR6 \| pdb_00001wr6	Download File View File

Crystal structure of GGA3 GAT domain in complex with ubiquitin

Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) Genes Cells 10: 639-654

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA3 (protein) ubiquitin (protein)

Explore in 3D

2A68 \| pdb_00002a68	Download File View File

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin

Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Cell 122: 351-363

Released	2005-09-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA polymerase omega chain (protein) RNA polymerase sigma factor rpoD (protein)
Unique Ligands	MG, RBT, ZN

Explore in 3D

2A69 \| pdb_00002a69	Download File View File

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin

Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Cell 122: 351-363

Released	2005-09-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA polymerase omega chain (protein) RNA polymerase sigma factor rpoD (protein)
Unique Ligands	MG, RPT, ZN

Explore in 3D

2A6E \| pdb_00002a6e	Download File View File

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme

Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Cell 122: 351-363

Released	2005-09-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA polymerase omega chain (protein) RNA polymerase sigma factor rpoD (protein)
Unique Ligands	MG, ZN

Explore in 3D

2A6H \| pdb_00002a6h	Download File View File

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin

Temiakov, D., Zenkin, N., Vassylyeva, M.N., Perederina, A., Tahirov, T.H., Savkina, M., Zorov, S., Nikiforov, V., Igarashi, N., Matsugaki, N., Wakatsuki, S., Severinov, K., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Mol Cell 19: 655-666

Released	2005-09-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA polymerase omega chain (protein) RNA polymerase sigma factor rpoD (protein)
Unique Ligands	MG, STD, ZN

Explore in 3D

2BE5 \| pdb_00002be5	Download File View File

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin

Vassylyev, D.G., Svetlov, V., Vassylyeva, M.N., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Artsimovitch, I., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Nat Struct Mol Biol 12: 1086-1093

Released	2005-11-08
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	DNA-directed RNA polymerase alpha chain (protein) DNA-directed RNA polymerase beta chain (protein) DNA-directed RNA polymerase beta' chain (protein) RNA polymerase omega chain (protein) RNA polymerase sigma factor rpoD (protein)
Unique Ligands	MG, TGT, ZN

Explore in 3D

3AI4 \| pdb_00003ai4	Download File View File

Crystal structure of yeast enhanced green fluorescent protein - mouse polymerase iota ubiquitin binding motif fusion protein

Suzuki, N., Wakatsuki, S., Kawasaki, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1059-1066

Released	2010-09-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Aequorea victoria Mus musculus
Macromolecule	yeast enhanced green fluorescent protein,DNA polymerase iota (protein)
Unique Ligands	SO4

Explore in 3D

3AI5 \| pdb_00003ai5	Download File View File

Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein

Suzuki, N., Wakatsuki, S., Kawasaki, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1059-1066

Released	2010-09-29
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Aequorea victoria Mus musculus
Macromolecule	yeast enhanced green fluorescent protein,Ubiquitin (protein)
Unique Ligands	EDO

Explore in 3D

3U3P \| pdb_00003u3p	Download File View File

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 521-530

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor receptor superfamily member 21 (protein)

Explore in 3D

3U3Q \| pdb_00003u3q	Download File View File

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 521-530

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor receptor superfamily member 21 (protein)

Explore in 3D

3U3S \| pdb_00003u3s	Download File View File

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 521-530

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor receptor superfamily member 21 (protein)

Explore in 3D

3U3T \| pdb_00003u3t	Download File View File

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 521-530

Released	2012-05-02
Method	X-RAY DIFFRACTION 3.21 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor receptor superfamily member 21 (protein)

Explore in 3D

3U3V \| pdb_00003u3v	Download File View File

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

Ru, H., Zhao, L.X., Ding, W., Jiao, L.Y., Shaw, N., Zhang, L.G., Hung, L.W., Matsugaki, N., Wakatsuki, S., Liu, Z.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 521-530

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.96 Å
Organisms	Homo sapiens
Macromolecule	Tumor necrosis factor receptor superfamily member 21 (protein)

Explore in 3D

4YSC \| pdb_00004ysc	Download File View File

Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CL, CU

Explore in 3D

4YSE \| pdb_00004yse	Download File View File

High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CU, MPD

Explore in 3D

5D4H \| pdb_00005d4h	Download File View File

High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CU, GOL, NO2

Explore in 3D

5D4I \| pdb_00005d4i	Download File View File

Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU, NO2

Explore in 3D

5D4J \| pdb_00005d4j	Download File View File

Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	ACY, CL, CU, GOL

Explore in 3D

5F7A \| pdb_00005f7a	Download File View File

Nitrite complex structure of copper nitrite reductase from Alcaligenes faecalis determined at 293 K

Fukuda, Y., Tse, K.M., Nakane, T., Nakatsu, T., Suzuki, M., Sugahara, M., Inoue, S., Masuda, T., Yumoto, F., Matsugaki, N., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Murphy, M.E.P., Inoue, T., Iwata, S., Mizohata, E.

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CU, NO2

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1IU1 | pdb_00001iu1

1J2J | pdb_00001j2j

1JWF | pdb_00001jwf

1JWG | pdb_00001jwg

1O3X | pdb_00001o3x

1O3Y | pdb_00001o3y

1WR6 | pdb_00001wr6

2A68 | pdb_00002a68

2A69 | pdb_00002a69

2A6E | pdb_00002a6e

2A6H | pdb_00002a6h

2BE5 | pdb_00002be5

3AI4 | pdb_00003ai4

3AI5 | pdb_00003ai5

3U3P | pdb_00003u3p

3U3Q | pdb_00003u3q

3U3S | pdb_00003u3s

3U3T | pdb_00003u3t

3U3V | pdb_00003u3v

4YSC | pdb_00004ysc

4YSE | pdb_00004yse

5D4H | pdb_00005d4h

5D4I | pdb_00005d4i

5D4J | pdb_00005d4j

5F7A | pdb_00005f7a