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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Song, J.M."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Lactobacillus acidophilus (4)
	Thermotoga maritima MSB8 (4)
	Vibrio cholerae (4)
	Homo sapiens (3)
	Staphylococcus aureus (2)
	Zymomonas mobilis (2)
	Vibrio vulnificus YJ016 (1)

Taxonomy

	Bacteria (17)
	Eukaryota (3)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (8)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (2)
	2.5 - 3.0 (3)
	3.0 - 3.5 (9)
	3.5 - 4.0 (2)

Release Date

	2010 - 2014 (3)
	2015 - 2019 (4)
	2020 - 2024 (10)

Enzyme Classification Name

	Hydrolases (1)
	Oxidoreductases (2)
	Translocases (1)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (13)
	MemProtMD (10)
	OPM (8)
	mpstruc (8)

Symmetry Type

	Cyclic (10)
	Asymmetric (7)

SCOP Classification

	Multi-domain proteins (alpha and beta) (2)
	All beta proteins (1)

AllSelected

1 to 17 of 17 Structures

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3OWO \| pdb_00003owo	Download File View File

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD cofactor

Moon, J.H., Lee, H.J., Song, J.M., Park, S.Y., Park, M.Y., Park, H.M., Sun, J., Park, J.H., Kim, J.S.

(2011) J Mol Biology 407: 413-424

Released	2011-02-16
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Zymomonas mobilis
Macromolecule	Alcohol dehydrogenase 2 (protein)
Unique Ligands	FE2

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3OX4 \| pdb_00003ox4	Download File View File

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 complexed with NAD cofactor

Moon, J.H., Lee, H.J., Song, J.M., Park, S.Y., Park, M.Y., Park, H.M., Sun, J., Park, J.H., Kim, J.S.

(2011) J Mol Biology 407: 413-424

Released	2011-02-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Zymomonas mobilis
Macromolecule	Alcohol dehydrogenase 2 (protein)
Unique Ligands	FE2, NAD

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3UFB \| pdb_00003ufb	Download File View File

Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1570-1577

Released	2012-11-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Vibrio vulnificus YJ016
Macromolecule	Type I restriction-modification system methyltransferase subunit (protein)

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4ZIR \| pdb_00004zir	Download File View File

Crystal structure of EcfAA' heterodimer bound to AMPPNP

Karpowich, N.K., Cocco, N., Song, J.M., Wang, D.N.

(2015) Nat Struct Mol Biol 22: 565-571

Released	2015-06-10
Method	X-RAY DIFFRACTION 3 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Energy-coupling factor transporter ATP-binding protein EcfA1 (protein) Energy-coupling factor transporter ATP-binding protein EcfA2 (protein)
Unique Ligands	ANP, CL, MG

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5KBW \| pdb_00005kbw	Download File View File

Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter

Karpowich, N.K., Wang, D.N., Song, J.M.

(2016) J Mol Biology 428: 3118-3130

Released	2016-06-29
Method	X-RAY DIFFRACTION 2.6093 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Riboflavin transporter RibU (protein)
Unique Ligands	RBF

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5KC0 \| pdb_00005kc0	Download File View File

Crystal structure of TmRibU, hexagonal crystal form

Karpowich, N.K., Wang, D.N., Song, J.M.

(2016) J Mol Biology 428: 3118-3130

Released	2016-06-29
Method	X-RAY DIFFRACTION 3.2001 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Riboflavin transporter RibU (protein)
Unique Ligands	BNG, RBF

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5KC4 \| pdb_00005kc4	Download File View File

Structure of TmRibU, orthorhombic crystal form

Karpowich, N.K., Wang, D.N., Song, J.M.

(2016) J Mol Biology 428: 3118-3130

Released	2016-06-29
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Riboflavin transporter RibU (protein)
Unique Ligands	BNG, RBF

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6WTW \| pdb_00006wtw	Download File View File

Structure of LaINDY crystallized in the presence of alpha-ketoglutarate and malate

Sauer, D.B., Cocco, N., Marden, J.J., Song, J.M., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

(2020) Elife 9:

Released	2020-09-16
Method	X-RAY DIFFRACTION 2.86 Å
Organisms	Lactobacillus acidophilus
Macromolecule	DASS family sodium-coupled anion symporter (protein)

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6WU1 \| pdb_00006wu1	Download File View File

Structure of apo LaINDY

Sauer, D.B., Marden, J.J., Cocco, N.C., Song, J.M., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

(2020) Elife 9:

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.09 Å
Organisms	Lactobacillus acidophilus
Macromolecule	DASS family sodium-coupled anion symporter (protein)
Unique Ligands	D10, HEX, OCT

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6WU2 \| pdb_00006wu2	Download File View File

Structure of the LaINDY-malate complex

Sauer, D.B., Marden, J.J., Cocco, N., Song, J.M., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

(2020) Elife 9:

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.36 Å
Organisms	Lactobacillus acidophilus
Macromolecule	DASS family sodium-coupled anion symporter (protein)
Unique Ligands	D10, HEX, OCT

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6WU3 \| pdb_00006wu3	Download File View File

Structure of VcINDY-Na+ in amphipol

Sauer, D.B., Marden, J.J., Song, J.M., Wang, D.N.

(2020) Elife 9:

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Vibrio cholerae
Macromolecule	VcINDY (protein)

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6WU4 \| pdb_00006wu4	Download File View File

Structure of the LaINDY-alpha-ketoglutarate complex

Sauer, D.B., Marden, J.J., Cocco, N., Song, J.M., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

(2020) Elife 9:

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.71 Å
Organisms	Lactobacillus acidophilus
Macromolecule	DASS family sodium-coupled anion symporter (protein)

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6WW5 \| pdb_00006ww5	Download File View File

Structure of VcINDY-Na-Fab84 in nanodisc

Sauer, D.B., Marden, J., Song, J.M., Koide, A., Koide, S., Wang, D.N.

(2020) Elife 9:

Released	2020-09-16
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Homo sapiens Vibrio cholerae
Macromolecule	DASS family sodium-coupled anion symporter (protein) Fab84 Heavy Chain (protein) Fab84 Light Chain (protein)
Unique Ligands	6PE, HEX, OCT

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7LO7 \| pdb_00007lo7	Download File View File

NorA in complex with Fab25

Brawley, D.N., Sauer, D.B., Song, J.M., Koide, A., Koide, S., Traaseth, N.J., Wang, D.N.

(2022) Nat Chem Biol 18: 706-712

Released	2022-04-20
Method	ELECTRON MICROSCOPY 3.74 Å
Organisms	Homo sapiens Staphylococcus aureus
Macromolecule	Fab25 Heavy Chain (protein) Fab25 Light Chain (protein) Quinolone resistance protein NorA (protein)

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7LO8 \| pdb_00007lo8	Download File View File

NorA in complex with Fab36

Brawley, D.N., Sauer, D.B., Song, J.M., Koide, A., Koide, S., Traaseth, N.J., Wang, D.N.

(2022) Nat Chem Biol 18: 706-712

Released	2022-04-20
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Homo sapiens Staphylococcus aureus
Macromolecule	Fab36 Heavy Chain (protein) Fab36 Light Chain (protein) Quinolone resistance protein NorA (protein)

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7T9F \| pdb_00007t9f	Download File View File

Structure of VcINDY-apo

Sauer, D.B., Marden, J.J., Song, J.M., Wang, D.N.

(2022) Nat Commun 13: 2644-2644

Released	2022-05-25
Method	ELECTRON MICROSCOPY 3.23 Å
Organisms	Vibrio cholerae
Macromolecule	DASS family sodium-coupled anion symporter (protein)

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7T9G \| pdb_00007t9g	Download File View File

Structure of VcINDY-Na+

Sauer, D.B., Marden, J.J., Song, J.M., Wang, D.N.

(2022) Nat Commun 13: 2644-2644

Released	2022-05-25
Method	ELECTRON MICROSCOPY 2.83 Å
Organisms	Vibrio cholerae
Macromolecule	DASS family sodium-coupled anion symporter (protein)
Unique Ligands	NA

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.

3OWO | pdb_00003owo

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD cofactor

3OX4 | pdb_00003ox4

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 complexed with NAD cofactor

3UFB | pdb_00003ufb

Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

4ZIR | pdb_00004zir

Crystal structure of EcfAA' heterodimer bound to AMPPNP

5KBW | pdb_00005kbw

Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter

5KC0 | pdb_00005kc0

Crystal structure of TmRibU, hexagonal crystal form

5KC4 | pdb_00005kc4

Structure of TmRibU, orthorhombic crystal form

6WTW | pdb_00006wtw

Structure of LaINDY crystallized in the presence of alpha-ketoglutarate and malate

6WU1 | pdb_00006wu1

Structure of apo LaINDY

6WU2 | pdb_00006wu2

Structure of the LaINDY-malate complex

6WU3 | pdb_00006wu3

Structure of VcINDY-Na+ in amphipol

6WU4 | pdb_00006wu4

Structure of the LaINDY-alpha-ketoglutarate complex

6WW5 | pdb_00006ww5

Structure of VcINDY-Na-Fab84 in nanodisc

7LO7 | pdb_00007lo7

NorA in complex with Fab25

7LO8 | pdb_00007lo8

NorA in complex with Fab36

7T9F | pdb_00007t9f

Structure of VcINDY-apo

7T9G | pdb_00007t9g

Structure of VcINDY-Na+

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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

3OWO | pdb_00003owo

3OX4 | pdb_00003ox4

3UFB | pdb_00003ufb

4ZIR | pdb_00004zir

5KBW | pdb_00005kbw

5KC0 | pdb_00005kc0

5KC4 | pdb_00005kc4

6WTW | pdb_00006wtw

6WU1 | pdb_00006wu1

6WU2 | pdb_00006wu2

6WU3 | pdb_00006wu3

6WU4 | pdb_00006wu4

6WW5 | pdb_00006ww5

7LO7 | pdb_00007lo7

7LO8 | pdb_00007lo8

7T9F | pdb_00007t9f

7T9G | pdb_00007t9g