RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Nogi, T."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 48 Structures.

Refinements

Structure Determination Methodology

experimental (48)

Scientific Name of Source Organism

	Homo sapiens (20)
	Mus musculus (17)
	Aquifex aeolicus VF5 (11)
	Rattus norvegicus (10)
	Kangiella koreensis DSM 16069 (3)
	Thermochromatium tepidum (3)
	Bos taurus (2)
	Escherichia coli (2)
	Aquifex aeolicus (1)
	Escherichia coli K-12 (1)

Taxonomy

	Eukaryota (39)
	Bacteria (20)
	Eukaryota (eukaryotes) (2)

Experimental Method

	X-RAY DIFFRACTION (46)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (48)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (2)
	1.5 - 2.0 (7)
	2.0 - 2.5 (13)
	2.5 - 3.0 (8)
	3.0 - 3.5 (11)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	2000 - 2004 (9)
	2005 - 2009 (5)
	2010 - 2014 (10)
	2015 - 2019 (10)
	2020 - 2024 (11)
	2025 - 2029 (3)

Enzyme Classification Name

Hydrolases (23)

Membrane Protein Annotation

	PDBTM (6)
	OPM (4)
	mpstruc (3)
	MemProtMD (2)

Symmetry Type

	Asymmetric (44)
	Cyclic (8)

SCOP Classification

	All beta proteins (7)
	All alpha proteins (5)
	Alpha and beta proteins (a/b) (2)
	Artifacts (2)
	Membrane and cell surface proteins and peptides (1)
	Small proteins (2)

AllSelected

1 to 25 of 48 Structures

Page 1 of 2

Sort by

Explore in 3D

1EYS \| pdb_00001eys	Download File View File

CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM

Nogi, T., Fathir, I., Kobayashi, M., Nozawa, T., Miki, K.

(2000) Proc Natl Acad Sci U S A 97: 13561-13566

Released	2000-12-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermochromatium tepidum
Macromolecule	PHOTOSYNTHETIC REACTION CENTER (protein)
Unique Ligands	BCL, BGL, BPH, CRT, FE, HEM, LDA, MQ8, PEF

Explore in 3D

1EYT \| pdb_00001eyt	Download File View File

CRYSTAL STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM TEPIDUM

Nogi, T., Fathir, I., Kobayashi, M., Nozawa, T., Miki, K.

(2000) Proc Natl Acad Sci U S A 97: 13561-13566

Released	2000-12-13
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Thermochromatium tepidum
Macromolecule	HIGH-POTENTIAL IRON-SULFUR PROTEIN (protein)
Unique Ligands	SF4

Explore in 3D

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

1IUA \| pdb_00001iua	Download File View File

Ultra-high resolution structure of HiPIP from Thermochromatium tepidum

Liu, L., Nogi, T., Kobayashi, M., Nozawa, T., Miki, K.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1085-1091

Released	2002-03-20
Method	X-RAY DIFFRACTION 0.8 Å
Organisms	Thermochromatium tepidum
Macromolecule	High-potential iron-sulfur protein (protein)
Unique Ligands	SF4, SO4

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

2DDU \| pdb_00002ddu	Download File View File

Crystal structure of the third repeat domain of reelin

Nogi, T., Yasui, N., Takagi, J.

(2006) EMBO J 25: 3675-3683

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Mus musculus
Macromolecule	reelin (protein)
Unique Ligands	CA, CL, MG

Explore in 3D

2E26 \| pdb_00002e26	Download File View File

Crystal structure of two repeat fragment of reelin

Yasui, N., Nogi, T., Kitao, T., Takagi, J.

(2007) Proc Natl Acad Sci U S A 104: 9988-9993

Released	2007-05-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	Reelin (protein)
Unique Ligands	ACT, CA, NAG, ZN
Unique branched monosaccharides	BMA, NAG

Explore in 3D

2ZOT \| pdb_00002zot	Download File View File

Crystal structure of human F-spondin reeler domain (fragment 1)

Nagae, M., Nogi, T., Takagi, J.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1138-1145

Released	2008-10-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Spondin-1 (protein)

Explore in 3D

2ZOU \| pdb_00002zou	Download File View File

Crystal structure of human F-spondin reeler domain (fragment 2)

Nagae, M., Nogi, T., Takagi, J.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1138-1145

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Spondin-1 (protein)
Unique Ligands	EDO

Explore in 3D

2ZPK \| pdb_00002zpk	Download File View File

Crystal structure of P20.1 Fab fragment in complex with its antigen peptide

Nogi, T., Sanagawa, T., Takagi, J.

(2008) Protein Sci 17: 2120-2126

Released	2008-12-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	IgG1-lambda P20.1 Fab (heavy chain) (protein) IgG1-lambda P20.1 Fab (light chain) (protein) Proteinase-activated receptor 4 (protein)
Unique Ligands	GOL

Explore in 3D

3A7Q \| pdb_00003a7q	Download File View File

Structural basis for specific recognition of reelin by its receptors

Yasui, N., Nogi, T., Takagi, J.

(2010) Structure 18: 320-331

Released	2010-03-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Low-density lipoprotein receptor-related protein 8 (protein) Reelin (protein)
Unique Ligands	CA, NAG, ZN
Unique branched monosaccharides	NAG

Explore in 3D

3AFC \| pdb_00003afc	Download File View File

Mouse Semaphorin 6A extracellular domain

Yasui, N., Nogi, T., Mihara, E., Takagi, J.

(2010) Nature 467: 1123-1127

Released	2010-10-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus
Macromolecule	Semaphorin-6A (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

Explore in 3D

3AL8 \| pdb_00003al8	Download File View File

Plexin A2 / Semaphorin 6A complex

Nogi, T., Yasui, N., Mihara, E., Takagi, J.

(2010) Nature 467: 1123-1127

Released	2010-10-06
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Mus musculus
Macromolecule	Plexin-A2 (protein) Semaphorin-6A (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

Explore in 3D

3AL9 \| pdb_00003al9	Download File View File

Mouse Plexin A2 extracellular domain

Nogi, T., Yasui, N., Mihara, E., Takagi, J.

(2010) Nature 467: 1123-1127

Released	2010-10-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Plexin-A2 (protein)
Unique Ligands	EDO, NAG

Explore in 3D

3ASI \| pdb_00003asi	Download File View File

Alpha-Neurexin-1 ectodomain fragment; LNS5-EGF3-LNS6

Tanaka, H., Nogi, T., Yasui, N., Takagi, J.

(2011) PLoS One 6: e19411-e19411

Released	2011-04-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	Neurexin-1-alpha (protein)
Unique Ligands	CA, NAG

Explore in 3D

3VI3 \| pdb_00003vi3	Download File View File

Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)

Nagae, M., Nogi, T., Takagi, J.

(2012) J Cell Biol 197: 131-140

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Integrin alpha-5 (protein) Integrin beta-1 (protein) SG/19 Fab fragment (Heavy chain) (protein) SG/19 Fab fragment (Light chain) (protein)
Unique Ligands	CA, MG, NAG
Unique branched monosaccharides	BMA, MAN, NAG

Explore in 3D

3VI4 \| pdb_00003vi4	Download File View File

Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide

Nagae, M., Nogi, T., Takagi, J.

(2012) J Cell Biol 197: 131-140

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Integrin alpha-5 (protein) Integrin beta-1 (protein) RGD peptide (protein) SG/19 Fab fragment (Heavy chain) (protein) SG/19 Fab fragment (Light chain) (protein)
Unique Ligands	CA, MG, NAG
Unique branched monosaccharides	BMA, MAN, NAG

Explore in 3D

3VKF \| pdb_00003vkf	Download File View File

Crystal Structure of Neurexin 1beta/Neuroligin 1 complex

Tanaka, H., Miyazaki, N., Nogi, T., Iwasaki, K., Takagi, J.

(2012) Cell Rep 2: 101-110

Released	2012-08-01
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Bos taurus Rattus norvegicus
Macromolecule	Neurexin-1-beta (protein) Neuroligin-1 (protein)
Unique Ligands	CA, NAG
Unique branched monosaccharides	BMA, NAG

Explore in 3D

3WKL \| pdb_00003wkl	Download File View File

The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus

Nogi, T., Tabata, S., Tamura-kawakami, K., Takagi, J.

(2013) Structure 22: 326-336

Released	2013-12-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Aquifex aeolicus
Macromolecule	Putative Zinc Metalloprotease AQ_1964 (protein)

Explore in 3D

3WKM \| pdb_00003wkm	Download File View File

The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus in complex with the Fab fragment

Nogi, T., Tabata, S., Tamura-kawakami, K., Takagi, J.

(2013) Structure 22: 326-336

Released	2013-12-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Aquifex aeolicus VF5 Mus musculus
Macromolecule	MOUSE IGG1-KAPPA FAB (HEAVY CHAIN) (protein) MOUSE IGG1-KAPPA FAB (LIGHT CHAIN) (protein) Putative zinc metalloprotease aq_1964 (protein)