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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Deb, I."

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Escherichia coli (7)
	synthetic construct (2)
	Bacillus subtilis (1)

Taxonomy

	Bacteria (7)
	other sequences (2)

Experimental Method

	ELECTRON MICROSCOPY (7)
	SOLUTION NMR (2)

Polymer Entity Type

	RNA (9)
	DNA (7)
	Protein (7)

Refinement Resolution (Å)

	3.0 - 3.5 (2)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (7)

Enzyme Classification Name

Transferases (7)

Symmetry Type

Asymmetric (7)

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1 to 9 of 9 Structures

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6I1V \| pdb_00006i1v	Download File View File

Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)

Deb, I., Popenda, L., Sarzynska, J., Gdaniec, Z.

(2019) Sci Rep 9: 16278-16278

Released	2019-11-20
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	RNA (5'-R(APCPUPCPAPGPUPGPA)-3') (nucleic acid) RNA (5'-R(UPCPAPCP(PSU)PGPAPGPU)-3') (nucleic acid)

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6I1W \| pdb_00006i1w	Download File View File

Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context)

Deb, I., Popenda, L., Sarzynska, J., Gdaniec, Z.

(2019) Sci Rep 9: 16278-16278

Released	2019-11-20
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	RNA (5'-R(APCPUPGPAPCPUPGPA)-3') (nucleic acid) RNA (5'-R(UPCPAPGP(PSU)PCPAPGPU)-3') (nucleic acid)

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8F3C \| pdb_00008f3c	Download File View File

Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG

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8G00 \| pdb_00008g00	Download File View File

Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 3
Unique Ligands	MG

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8G1S \| pdb_00008g1s	Download File View File

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Bacillus subtilis Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG

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8G2W \| pdb_00008g2w	Download File View File

Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG

Explore in 3D

8G4W \| pdb_00008g4w	Download File View File

Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG, PRF

Explore in 3D

8G7E \| pdb_00008g7e	Download File View File

Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

Porta, J.C., Chauvier, A., Deb, I., Ellinger, E., Frank, A.T., Meze, K., Ohi, M.D., Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG, PRF

Explore in 3D

8G8Z \| pdb_00008g8z	Download File View File

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

Porta, J.C., Ohi, M.D., Walter, N.G., Frank, A.T., Deb, I., Meze, K.

(2023) Nat Struct Mol Biol 30: 902-913

Released	2023-06-21
Method	ELECTRON MICROSCOPY 4.3 Å
Organisms	Escherichia coli
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 3
Unique Ligands	MG, PRF

1 to 9 of 9 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.

6I1V | pdb_00006i1v

Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)

6I1W | pdb_00006i1w

Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context)

8F3C | pdb_00008f3c

Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

8G00 | pdb_00008g00

Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

8G1S | pdb_00008g1s

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

8G2W | pdb_00008g2w

Cryo-EM structure of 3DVA component 2 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand

8G4W | pdb_00008g4w

Cryo-EM consensus structure of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

8G7E | pdb_00008g7e

Cryo-EM structure of 3DVA component 0 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

8G8Z | pdb_00008g8z

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase plus preQ1 ligand

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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

6I1V | pdb_00006i1v

6I1W | pdb_00006i1w

8F3C | pdb_00008f3c

8G00 | pdb_00008g00

8G1S | pdb_00008g1s

8G2W | pdb_00008g2w

8G4W | pdb_00008g4w

8G7E | pdb_00008g7e

8G8Z | pdb_00008g8z