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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Vibrio harveyi"

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Bordetella phage BPP-1 (9)
	Methylorubrum extorquens AM1 (7)
	Nanoarchaeota archaeon JGI OTU-1 (1)
	Thermus aquaticus Y51MC23 (1)

Taxonomy

	Duplodnaviria (9)
	Bacteria (8)
	Archaea (1)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (2)

Polymer Entity Type

	Protein (11)
	RNA (9)

Refinement Resolution (Å)

	2.5 - 3.0 (2)
	3.0 - 3.5 (8)
	3.5 - 4.0 (1)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (9)

Enzyme Classification Name

Lyases (9)

Symmetry Type

Asymmetric (11)

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1 to 11 of 11 Structures

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5IOO	Download File View File

Accommodation of massive sequence variation in Nanoarchaeota by the C-type lectin fold

Handa, S., Paul, B., Miller, J., Valentine, D., Ghosh, P.

(2016) BMC Struct Biol 16: 13-13

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.521 Å
Organisms	Nanoarchaeota archaeon JGI OTU-1
Macromolecule	AvpA (protein)
Unique Ligands	MG

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5VF4	Download File View File

Thermus aquaticus variable protein (TaqVP) from diversity-generating retroelements (DGR)

Handa, S., Ghosh, P.

(2019) PLoS One 14: e0205618-e0205618

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Thermus aquaticus Y51MC23
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	ACT, CA

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8UB7	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Active state (N-occupied)

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)
Unique Ligands	DCP, MG

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8UB8	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active State 1a

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.28 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UB9	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase- Active state (N-empty) 1a

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.07 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UBA	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active state 1b

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UBB	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Active State (N-empty) 1b

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.23 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UBC	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Resting State 1b

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.29 Å
Organisms	Bordetella phage BPP-1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid)

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8UBD	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active State 2

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.05 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UBE	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Resting State 1a

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.05 Å
Organisms	Bordetella phage BPP-1 Methylorubrum extorquens AM1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid) Diversity-generating retroelement (DGR) RNA avd (nucleic acid)

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8UBF	Download File View File

Diversity-generating retroelement (DGR) ribonucleoprotein - Resting state 1c

Biswas, T., Handa, S., Ghosh, P.

(2025) Nature

Released	2024-10-23
Method	ELECTRON MICROSCOPY 3.61 Å
Organisms	Bordetella phage BPP-1
Macromolecule	Avd (protein) Reverse transcriptase (protein) Diversity-generating retroelement (DGR) RNA Sp (nucleic acid) Diversity-generating retroelement (DGR) RNA TR (nucleic acid)

1 to 11 of 11 Structures

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