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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Tsutsumi, N."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Homo sapiens (16)
	Mus musculus (8)
	Human betaherpesvirus 5 (5)
	synthetic construct (2)
	Escherichia coli (1)
	Human herpesvirus 5 strain AD169 (1)
	Lama glama (1)
	Xenopus laevis (1)
	human gammaherpesvirus 4 (1)

Taxonomy

	Eukaryota (17)
	Duplodnaviria (7)
	other sequences (2)
	Bacteria (1)

Experimental Method

	ELECTRON MICROSCOPY (12)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (1)
	3.0 - 3.5 (6)
	3.5 - 4.0 (8)
	4.0 - 4.5 (1)

Release Date

	2010 - 2014 (3)
	2015 - 2019 (1)
	2020 - 2024 (13)

Enzyme Classification Name

	Hydrolases (8)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (8)
	MemProtMD (7)
	OPM (7)
	mpstruc (6)

Symmetry Type

	Asymmetric (15)
	Cyclic (2)

SCOP Classification

All beta proteins (3)

AllSelected

1 to 17 of 17 Structures

Page 1 of 1

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Explore in 3D

3WO2 \| pdb_00003wo2	Download File View File

Crystal structure of human interleukin-18

Tsutsumi, N., Kimura, T., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato, Z., Tochio, H.

(2014) Nat Commun 5: 5340-5340

Released	2014-12-17
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-18 (protein)
Unique Ligands	CPS, SO4

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3WO3 \| pdb_00003wo3	Download File View File

Crystal structure of IL-18 in complex with IL-18 receptor alpha

Tsutsumi, N., Kimura, T., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato, Z., Tochio, H.

(2014) Nat Commun 5: 5340-5340

Released	2014-12-17
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-18 (protein) Interleukin-18 receptor 1 (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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3WO4 \| pdb_00003wo4	Download File View File

Crystal structure of the IL-18 signaling ternary complex

Tsutsumi, N., Kimura, T., Arita, K., Ariyoshi, M., Ohnishi, H., Kondo, N., Shirakawa, M., Kato, Z., Tochio, H.

(2014) Nat Commun 5: 5340-5340

Released	2014-12-17
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-18 (protein) Interleukin-18 receptor 1 (protein) Interleukin-18 receptor accessory protein (protein)
Unique Ligands	CL, NAG
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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5WB2 \| pdb_00005wb2	Download File View File

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

Jude, K.M., Burg, J.S., Tsutsumi, N., Miles, T.F., Garcia, K.C.

(2018) Elife 7:

Released	2018-06-13
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Lama glama synthetic construct
Macromolecule	CX3CL1 protein (protein) Envelope protein US28, nanobody 7 fusion protein (protein) nanobody B1 (protein)
Unique Ligands	CLR, MES, OLC, ZN

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6WW2 \| pdb_00006ww2	Download File View File

Structure of human Frizzled5 by fiducial-assisted cryo-EM

Tsutsumi, N., Jude, K.M., Gati, C., Garcia, K.C.

(2020) Elife 9:

Released	2020-08-19
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Escherichia coli Homo sapiens synthetic construct
Macromolecule	Frizzled-5,Soluble cytochrome b562 (protein) anti-BRIL Fab Heavy chain (protein) anti-BRIL Fab Light chain (protein) anti-Fab Nanobody (protein)

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6X93 \| pdb_00006x93	Download File View File

Interleukin-10 signaling complex with IL-10RA and IL-10RB

Saxton, R.A., Tsutsumi, N., Gati, C., Garcia, K.C.

(2021) Science 371:

Released	2021-03-17
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-10 (protein) Interleukin-10 receptor subunit alpha (protein) Interleukin-10 receptor subunit beta (protein)

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7JHJ \| pdb_00007jhj	Download File View File

Structure of the Epstein-Barr virus GPCR BILF1 in complex with human Gi

Tsutsumi, N., Qu, Q.H., Skiniotis, G., Garcia, K.C.

(2021) Immunity 54: 1405-1416.e7

Released	2021-07-07
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Mus musculus human gammaherpesvirus 4
Macromolecule	Antibody fragment scFv16 (protein) BILF1 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein)
Unique Ligands	Y01

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7RKF \| pdb_00007rkf	Download File View File

Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

Tsutsumi, N., Maeda, S., Qu, Q., Skiniotis, G., Kobilka, B.K., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Mus musculus
Macromolecule	Unique protein chains: 6
Unique Ligands	GDP, NAG

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7RKM \| pdb_00007rkm	Download File View File

Structure of CX3CL1-US28-Gi-scFv16 in C-state

Tsutsumi, N., Qu, Q., Jude, K.M., Skiniotis, G., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Mus musculus
Macromolecule	Unique protein chains: 6
Unique Ligands	CLR

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7RKN \| pdb_00007rkn	Download File View File

Structure of CX3CL1-US28-Gi-scFv16 in OC-state

Tsutsumi, N., Qu, Q., Jude, K.M., Skiniotis, G., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens Human herpesvirus 5 strain AD169 Mus musculus
Macromolecule	Unique protein chains: 6

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7RKX \| pdb_00007rkx	Download File View File

Structure of US27-Gi-scFv16 in CL-state

Tsutsumi, N., Jude, K.M., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Mus musculus
Macromolecule	Antibody fragment scFv16 (protein) G-protein coupled receptor homolog US27 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein)

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7RKY \| pdb_00007rky	Download File View File

Binding mode of US27-Gi-scFv16 in OCL-state

Tsutsumi, N., Jude, K.M., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens Human betaherpesvirus 5 Mus musculus
Macromolecule	Antibody fragment scFv16 (protein) G-protein coupled receptor homolog US27 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Guanine nucleotide-binding protein G(i) subunit alpha-1 (protein)
Unique Ligands	GDP

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7T6F \| pdb_00007t6f	Download File View File

Structure of active Janus Kinase (JAK) dimer complexed with cytokine receptor intracellular domain

Glassman, C.R., Tsutsumi, N., Jude, K.M., Garcia, K.C.

(2022) Science 376: 163-169

Released	2022-03-16
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Mus musculus
Macromolecule	Interferon lambda receptor 1 (protein) Tyrosine-protein kinase (protein)
Unique Ligands	ADN, ADP

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7U7N \| pdb_00007u7n	Download File View File

IL-27 quaternary receptor signaling complex

Caveney, N.A., Glassman, C.R., Jude, K.M., Tsutsumi, N., Garcia, K.C.

(2022) Elife 11:

Released	2022-05-25
Method	ELECTRON MICROSCOPY 3.47 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-27 receptor subunit alpha (protein) Interleukin-27 subunit alpha (protein) Interleukin-27 subunit beta (protein) Interleukin-6 receptor subunit beta (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8CTG \| pdb_00008ctg	Download File View File

Extracellular architecture of an engineered canonical Wnt signaling ternary complex

Tsutsumi, N., Jude, K.M., Garcia, K.C.

(2023) Proc Natl Acad Sci U S A 120: e2218238120-e2218238120

Released	2023-03-15
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens Mus musculus Xenopus laevis
Macromolecule	Frizzled-8 (protein) Low-density lipoprotein receptor-related protein 6 (protein) Protein Wnt-8 (protein)
Unique Ligands	PAM

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8FFE \| pdb_00008ffe	Download File View File

Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide

Jude, K.M., Tsutsumi, N., Waghray, D., Garcia, K.C.

(2023) Proc Natl Acad Sci U S A 120: e2218238120-e2218238120

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Homo sapiens
Macromolecule	Low-density lipoprotein receptor-related protein 6 (protein) YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker (protein) YW210.09 Fab light chain (protein)
Unique Ligands	GOL, NA, SIN
Unique branched monosaccharides	BMA, FUC, MAN, NAG

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8G04 \| pdb_00008g04	Download File View File

Structure of signaling thrombopoietin-MPL receptor complex

Tsutsumi, N., Jude, K.M., Gati, C., Garcia, K.C.

(2023) Cell 186: 4189-4203.e22

Released	2023-08-30
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Homo sapiens
Macromolecule	Thrombopoietin (protein) Thrombopoietin receptor (protein)
Unique Ligands	MAN, NAG

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.

3WO2 | pdb_00003wo2

Crystal structure of human interleukin-18

3WO3 | pdb_00003wo3

Crystal structure of IL-18 in complex with IL-18 receptor alpha

3WO4 | pdb_00003wo4

Crystal structure of the IL-18 signaling ternary complex

5WB2 | pdb_00005wb2

US28 bound to engineered chemokine CX3CL1.35 and nanobodies

6WW2 | pdb_00006ww2

Structure of human Frizzled5 by fiducial-assisted cryo-EM

6X93 | pdb_00006x93

Interleukin-10 signaling complex with IL-10RA and IL-10RB

7JHJ | pdb_00007jhj

Structure of the Epstein-Barr virus GPCR BILF1 in complex with human Gi

7RKF | pdb_00007rkf

Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

7RKM | pdb_00007rkm

Structure of CX3CL1-US28-Gi-scFv16 in C-state

7RKN | pdb_00007rkn

Structure of CX3CL1-US28-Gi-scFv16 in OC-state

7RKX | pdb_00007rkx

Structure of US27-Gi-scFv16 in CL-state

7RKY | pdb_00007rky

Binding mode of US27-Gi-scFv16 in OCL-state

7T6F | pdb_00007t6f

Structure of active Janus Kinase (JAK) dimer complexed with cytokine receptor intracellular domain

7U7N | pdb_00007u7n

IL-27 quaternary receptor signaling complex

8CTG | pdb_00008ctg

Extracellular architecture of an engineered canonical Wnt signaling ternary complex

8FFE | pdb_00008ffe

Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide

8G04 | pdb_00008g04

Structure of signaling thrombopoietin-MPL receptor complex

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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

3WO2 | pdb_00003wo2

3WO3 | pdb_00003wo3

3WO4 | pdb_00003wo4

5WB2 | pdb_00005wb2

6WW2 | pdb_00006ww2

6X93 | pdb_00006x93

7JHJ | pdb_00007jhj

7RKF | pdb_00007rkf

7RKM | pdb_00007rkm

7RKN | pdb_00007rkn

7RKX | pdb_00007rkx

7RKY | pdb_00007rky

7T6F | pdb_00007t6f

7U7N | pdb_00007u7n

8CTG | pdb_00008ctg

8FFE | pdb_00008ffe

8G04 | pdb_00008g04