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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Candidatus Odinarchaeum yellowstonii"

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Candidatus Odinarchaeum yellowstonii (19)
	Oryctolagus cuniculus (1)

Taxonomy

	Archaea (19)
	Eukaryota (1)

Experimental Method

X-RAY DIFFRACTION (19)

Polymer Entity Type

Protein (19)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (8)
	2.0 - 2.5 (4)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)

Release Date

	2015 - 2019 (1)
	2020 - 2024 (18)

Enzyme Classification Name

	Transferases (5)
	Hydrolases (1)

Symmetry Type

	Asymmetric (13)
	Cyclic (6)

SCOP Classification

Alpha and beta proteins (a/b) (1)

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1 to 19 of 19 Structures

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5ZZA \| pdb_00005zza	Download File View File

OdinProfilin/Rabbit Actin Complex

Robinson, R.C., Akil, C.

(2018) Nature 562: 439-443

Released	2018-10-10
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Candidatus Odinarchaeum yellowstonii Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein) Uncharacterized protein (protein)
Unique Ligands	ATP, CA, LAB

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7EVB \| pdb_00007evb	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 77% GTP/23% and 2 Na+

Robinson, R.C., Akil, C.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, NA

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7EVC \| pdb_00007evc	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 60% GTP/40% GDP and 2 Na+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, NA

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7EVD \| pdb_00007evd	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 53% GTP/47% and 2 Na+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, NA

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7EVE \| pdb_00007eve	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 100% GDP and 2 Na+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, NA

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7EVG \| pdb_00007evg	Download File View File

Apo Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a psuedo-protofilament arrangement

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 2.48 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	PO4

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7EVH \| pdb_00007evh	Download File View File

Odinarchaeota tubulin H393D mutant, in a psuedo protofilament arrangement, bound to 59% GDP, 41% phosphate

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, PO4

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7EVI \| pdb_00007evi	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 79% GTP, 21% GDP, Na+, Mg2+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, MG, NA

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7EVK \| pdb_00007evk	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 78% GTP, 22% GDP, Na+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, NA

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7EVL \| pdb_00007evl	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 64% GTP/36% GDP and 2 Na+ in a small unit cell

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, NA

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7F1A \| pdb_00007f1a	Download File View File

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound 78% GTP/22% GDP 1 K+, 1 Mg2+

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, GTP, K, MG

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7F1B \| pdb_00007f1b	Download File View File

Odinarchaeota tubulin H393D mutant, in a pseudo protofilament arrangement, after GTP hydrolysis and phosphate release

Robinson, R.C., Akil, C., Tran, L.T.

(2022) Sci Adv 8: eabm2225-eabm2225

Released	2022-03-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tubulin-like protein (protein)
Unique Ligands	GDP, MG

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7F8F \| pdb_00007f8f	Download File View File

Roadblock from Odinarchaeota LCB_4

Robinson, R.C., Akil, C.

(2024) Commun Biol 7: 273

Released	2022-07-13
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Robl_LC7 domain-containing protein (protein)

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7OWE \| pdb_00007owe	Download File View File

Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a

Grundstrom, C., Aberg-Zingmark, E., Verma, A., Wolf-Watz, M., Sauer, U.H., Sauer-Eriksson, A.E.

(2022) Sci Adv 8: eabm4089-eabm4089

Released	2022-09-28
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Adenylate kinase (protein)
Unique Ligands	AP5

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7OWH \| pdb_00007owh	Download File View File

Odinarchaeota Adenylate kinase (OdinAK) native structure

Aberg-Zingmark, E., Grundstrom, C., Verma, A., Wolf-Watz, M., Sauer, U.H., Sauer-Eriksson, A.E.

(2022) Sci Adv 8: eabm4089-eabm4089

Released	2022-09-28
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Adenylate kinase (protein)
Unique Ligands	CL

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7OWJ \| pdb_00007owj	Download File View File

Odinarchaeota Adenylate kinase (OdinAK) in complex with GTP

Aberg-Zingmark, E., Grundstrom, C., Verma, A., Wolf-Watz, M., Sauer, U.H., Sauer-Eriksson, A.E.

(2022) Sci Adv 8: eabm4089-eabm4089

Released	2022-09-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Adenylate kinase (protein)
Unique Ligands	GTP

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7OWK \| pdb_00007owk	Download File View File

Odinarchaeota Adenylate kinase (OdinAK) in complex with dTTP

Aberg-Zingmark, E., Grundstrom, C., Verma, A., Wolf-Watz, M., Sauer, U.H., Sauer-Eriksson, A.E.

(2022) Sci Adv 8: eabm4089-eabm4089

Released	2022-09-28
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Adenylate kinase (protein)
Unique Ligands	TTP

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7OWL \| pdb_00007owl	Download File View File

Odinarchaeota Adenylate kinase (OdinAK) in complex with CTP

Aberg-Zingmark, E., Grundstrom, C., Verma, A., Wolf-Watz, M., Sauer, U.H., Sauer-Eriksson, A.E.

(2022) Sci Adv 8: eabm4089-eabm4089

Released	2022-09-28
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Adenylate kinase (protein)
Unique Ligands	CTP

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7PB9 \| pdb_00007pb9	Download File View File

Crystal structure of tandem WH domains of Vps25 from Odinarchaeota

Salzer, R., Bellini, D., Papatziamou, D., Robinson, N.P., Lowe, J.

(2022) Nat Commun 13: 3398-3398

Released	2022-06-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Candidatus Odinarchaeum yellowstonii
Macromolecule	Tandem WH domains of Vps25 (protein)

1 to 19 of 19 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.

5ZZA | pdb_00005zza

OdinProfilin/Rabbit Actin Complex

7EVB | pdb_00007evb

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 77% GTP/23% and 2 Na+

7EVC | pdb_00007evc

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 60% GTP/40% GDP and 2 Na+

7EVD | pdb_00007evd

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 53% GTP/47% and 2 Na+

7EVE | pdb_00007eve

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 100% GDP and 2 Na+

7EVG | pdb_00007evg

Apo Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a psuedo-protofilament arrangement

7EVH | pdb_00007evh

Odinarchaeota tubulin H393D mutant, in a psuedo protofilament arrangement, bound to 59% GDP, 41% phosphate

7EVI | pdb_00007evi

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 79% GTP, 21% GDP, Na+, Mg2+

7EVK | pdb_00007evk

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 78% GTP, 22% GDP, Na+

7EVL | pdb_00007evl

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 64% GTP/36% GDP and 2 Na+ in a small unit cell

7F1A | pdb_00007f1a

Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound 78% GTP/22% GDP 1 K+, 1 Mg2+

7F1B | pdb_00007f1b

Odinarchaeota tubulin H393D mutant, in a pseudo protofilament arrangement, after GTP hydrolysis and phosphate release

7F8F | pdb_00007f8f

Roadblock from Odinarchaeota LCB_4

7OWE | pdb_00007owe

Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a

7OWH | pdb_00007owh

Odinarchaeota Adenylate kinase (OdinAK) native structure

7OWJ | pdb_00007owj

Odinarchaeota Adenylate kinase (OdinAK) in complex with GTP

7OWK | pdb_00007owk

Odinarchaeota Adenylate kinase (OdinAK) in complex with dTTP

7OWL | pdb_00007owl

Odinarchaeota Adenylate kinase (OdinAK) in complex with CTP

7PB9 | pdb_00007pb9

Crystal structure of tandem WH domains of Vps25 from Odinarchaeota

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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

Symmetry Type

SCOP Classification

5ZZA | pdb_00005zza

7EVB | pdb_00007evb

7EVC | pdb_00007evc

7EVD | pdb_00007evd

7EVE | pdb_00007eve

7EVG | pdb_00007evg

7EVH | pdb_00007evh

7EVI | pdb_00007evi

7EVK | pdb_00007evk

7EVL | pdb_00007evl

7F1A | pdb_00007f1a

7F1B | pdb_00007f1b

7F8F | pdb_00007f8f

7OWE | pdb_00007owe

7OWH | pdb_00007owh

7OWJ | pdb_00007owj

7OWK | pdb_00007owk

7OWL | pdb_00007owl

7PB9 | pdb_00007pb9