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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Uchida, K."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Salmonella enterica subsp. enterica serovar Typhi str. CT18 (9)
	Salmonella enterica subsp. enterica serovar Typhi (4)
	Mus musculus (3)
	Escherichia coli BL21(DE3) (2)
	Homo sapiens (2)

Taxonomy

	Bacteria (15)
	Eukaryota (5)

Experimental Method

	X-RAY DIFFRACTION (14)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.5 - 2.0 (6)
	2.0 - 2.5 (6)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)

Release Date

	2010 - 2014 (4)
	2020 - 2024 (13)

Enzyme Classification Name

	Hydrolases (1)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (2)
	PDBTM (2)
	mpstruc (2)

Symmetry Type

	Cyclic (15)
	Asymmetric (2)

SCOP Classification

	Alpha and beta proteins (a+b) (1)
	Small proteins (2)
	All beta proteins (1)

AllSelected

1 to 17 of 17 Structures

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3K19 \| pdb_00003k19	Download File View File

OmpF porin

Kefala, G., Ahn, C., Krupa, M., Maslennikov, I., Kwiatkowski, W., Choe, S., Center for Structures of Membrane Proteins (CSMP)

(2010) Protein Sci 19: 1117-1125

Released	2010-04-14
Method	X-RAY DIFFRACTION 3.79 Å
Organisms	Escherichia coli BL21(DE3)
Macromolecule	Outer membrane protein F (protein)

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3K1B \| pdb_00003k1b	Download File View File

Structure of OmpF porin

Kefala, G., Ahn, C., Krupa, M., Maslennikov, I., Kwiatkowski, W., Choe, S., Center for Structures of Membrane Proteins (CSMP)

(2010) Protein Sci 19: 1117-1125

Released	2010-04-14
Method	X-RAY DIFFRACTION 4.39 Å
Organisms	Escherichia coli BL21(DE3)
Macromolecule	Outer membrane protein F (protein)

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4MID \| pdb_00004mid	Download File View File

Crystal Structure of Activin A/BMP2 chimera

Esquivies, L.

(2014) J Bone Miner Res 29: 1950-1959

Released	2014-05-07
Method	X-RAY DIFFRACTION 2.139 Å
Organisms	Homo sapiens
Macromolecule	AB204 Activin A/BMP2 chimera (protein)

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4N1D \| pdb_00004n1d	Download File View File

Nodal/BMP2 chimera NB250

Esquivies, L.

(2014) J Biological Chem 289: 1788-1797

Released	2013-12-04
Method	X-RAY DIFFRACTION 1.912 Å
Organisms	Homo sapiens
Macromolecule	Nodal/BMP2 chimera protein (protein)

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6P4M \| pdb_00006p4m	Download File View File

Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.802 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, SIA

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6P4N \| pdb_00006p4n	Download File View File

Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-6-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, SIA

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6P4P \| pdb_00006p4p	Download File View File

Salmonella typhi PltB Homopentamer N29K Mutant

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)

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6P4Q \| pdb_00006p4q	Download File View File

Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, SIA

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6P4R \| pdb_00006p4r	Download File View File

Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-6-Gal-beta-1-4-GlcNAc glycans

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, SIA

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6P4S \| pdb_00006p4s	Download File View File

Salmonella typhi PltB Homopentamer T65I Mutant

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)

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6P4T \| pdb_00006p4t	Download File View File

Salmonella typhi PltB Homopentamer T65I Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Hillpot, E.C., Yang, Y.A., Song, J.

(2020) Cell Host Microbe 27: 937-949.e6

Released	2020-03-25
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Putative pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, SIA

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6TYN \| pdb_00006tyn	Download File View File

Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Yang, Y.A., Song, J.

(2020) PLoS Pathog 16: e1008336-e1008336

Released	2020-02-12
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi
Macromolecule	Pertussis like toxin subunit B (protein)
Unique branched monosaccharides	5N6, GAL, NAG

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6TYO \| pdb_00006tyo	Download File View File

Salmonella Typhi PltB Homopentamer with Neu-5NAc-4OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Yang, Y.A., Song, J.

(2020) PLoS Pathog 16: e1008336-e1008336

Released	2020-02-12
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi
Macromolecule	Pertussis-like toxin subunit (protein)
Unique branched monosaccharides	GAL, NAG, PKM

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6TYQ \| pdb_00006tyq	Download File View File

Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-6-Gal-beta-1-4-GlcNAc Glycans

Nguyen, T., Milano, S.K., Yang, Y.A., Song, J.

(2020) PLoS Pathog 16: e1008336-e1008336

Released	2020-02-12
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhi
Macromolecule	Pertussis-like toxin subunit B (protein)
Unique branched monosaccharides	5N6, GAL, NAG

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6VX4 \| pdb_00006vx4	Download File View File

Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin

Nguyen, T., Song, J.

(2021) iScience 24: 102454-102454

Released	2021-02-24
Method	ELECTRON MICROSCOPY 3.12 Å
Organisms	Mus musculus Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Cytolethal distending toxin subunit B (protein) Pertussis like toxin subunit B (protein) Pertussis toxin-like subunit ArtA (protein) Variable Domain of Heavy Chain of Antibody TyTx11 (protein) Variable Domain of Kappa Chain of TyTx11 Antibody (protein)

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7K7H \| pdb_00007k7h	Download File View File

Density-fitted Model Structure of Antibody Variable Domains of TyTx1 in Complex with PltB pentamer of Typhoid Toxin

Nguyen, T., Feathers, J.R., Fromme, J.C., Song, J.

(2021) Cell Rep 36: 109654-109654

Released	2021-09-01
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Mus musculus Salmonella enterica subsp. enterica serovar Typhi str. CT18
Macromolecule	Fab Heavy Chain Variable Domain (protein) Fab Light Chain Variable Domain (protein) Pertussis like toxin subunit B (protein) Pertussis toxin-like subunit ArtA (protein)

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7K7I \| pdb_00007k7i	Download File View File

Density-fitted Model Structure of Antibody Variable Domains of TyTx4 in Complex with PltB pentamer of Typhoid Toxin

Nguyen, T., Feathers, J.R., Fromme, J.C., Song, J.

(2021) Cell Rep 36: 109654-109654

Released	2021-09-01
Method	ELECTRON MICROSCOPY 3.13 Å
Organisms	Mus musculus Salmonella enterica subsp. enterica serovar Typhi
Macromolecule	Fab Heavy Chain Variable Domain (protein) Fab Light Chain Variable Domain (protein) Putative pertussis-like toxin subunit (protein)

1 to 17 of 17 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3K19 | pdb_00003k19

OmpF porin

3K1B | pdb_00003k1b

Structure of OmpF porin

4MID | pdb_00004mid

Crystal Structure of Activin A/BMP2 chimera

4N1D | pdb_00004n1d

Nodal/BMP2 chimera NB250

6P4M | pdb_00006p4m

Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

6P4N | pdb_00006p4n

Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-6-Gal-beta-1-4-GlcNAc Glycans

6P4P | pdb_00006p4p

Salmonella typhi PltB Homopentamer N29K Mutant

6P4Q | pdb_00006p4q

Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

6P4R | pdb_00006p4r

Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-6-Gal-beta-1-4-GlcNAc glycans

6P4S | pdb_00006p4s

Salmonella typhi PltB Homopentamer T65I Mutant

6P4T | pdb_00006p4t

Salmonella typhi PltB Homopentamer T65I Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

6TYN | pdb_00006tyn

Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

6TYO | pdb_00006tyo

Salmonella Typhi PltB Homopentamer with Neu-5NAc-4OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

6TYQ | pdb_00006tyq

Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-6-Gal-beta-1-4-GlcNAc Glycans

6VX4 | pdb_00006vx4

Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin

7K7H | pdb_00007k7h

Density-fitted Model Structure of Antibody Variable Domains of TyTx1 in Complex with PltB pentamer of Typhoid Toxin

7K7I | pdb_00007k7i

Density-fitted Model Structure of Antibody Variable Domains of TyTx4 in Complex with PltB pentamer of Typhoid Toxin

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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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

3K19 | pdb_00003k19

3K1B | pdb_00003k1b

4MID | pdb_00004mid

4N1D | pdb_00004n1d

6P4M | pdb_00006p4m

6P4N | pdb_00006p4n

6P4P | pdb_00006p4p

6P4Q | pdb_00006p4q

6P4R | pdb_00006p4r

6P4S | pdb_00006p4s

6P4T | pdb_00006p4t

6TYN | pdb_00006tyn

6TYO | pdb_00006tyo

6TYQ | pdb_00006tyq

6VX4 | pdb_00006vx4

7K7H | pdb_00007k7h

7K7I | pdb_00007k7i