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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Waldo, G.S."

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

	synthetic construct (8)
	Severe acute respiratory syndrome coronavirus 2 (4)
	Influenza B virus (B/Memphis/13/2003) (3)
	Homo sapiens (2)
	Human immunodeficiency virus 1 (2)
	SFTS virus AH12 (2)
	Danio rerio (1)
	Equine encephalosis virus (1)
	Influenza A virus (1)
	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) (1)

More...

Taxonomy

	Riboviria (15)
	other sequences (8)
	Eukaryota (5)

Experimental Method

	X-RAY DIFFRACTION (11)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (2)

Polymer Entity Type

	RNA (18)
	Protein (16)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (2)
	2.5 - 3.0 (2)
	3.0 - 3.5 (5)
	3.5 - 4.0 (3)

Release Date

	2015 - 2019 (8)
	2020 - 2024 (10)

Enzyme Classification Name

	Transferases (14)
	Hydrolases (8)
	Lyases (1)

Symmetry Type

Asymmetric (16)

AllSelected

1 to 18 of 18 Structures

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5MSG	Download File View File

Influenza B polymerase bound to vRNA promoter and capped RNA primer

Cusack, S., Guilligay, D.

(2017) Nucleic Acids Res 45: 3353-3368

Released	2017-02-08
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Influenza B virus synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3
Unique Ligands	PO4

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6C6K	Download File View File

Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex

Amarasinghe, G.K., Leung, D.W., Johnson, B., Xu, W.

(2018) Immunity 48: 487-499.e5

Released	2018-04-04
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Equine encephalosis virus Homo sapiens
Macromolecule	Interferon-induced protein with tetratricopeptide repeats 1 (protein) Interferon-induced protein with tetratricopeptide repeats 3 (protein) RNA (5'-R((M7G)PAPUPAPGPGPCPGPGPCP*G)-3') (nucleic acid)
Unique Ligands	MG

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6EVJ	Download File View File

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and capped RNA primer

Pflug, A., Cusack, S.

(2018) Nucleic Acids Res 46: 956-971

Released	2017-12-13
Method	X-RAY DIFFRACTION 3.9 Å
Organisms	Influenza A virus Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3

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6IS0	Download File View File

Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH and m7G-capped RNA

Hirano, S., Nishimasu, H., Ishitani, R., Nureki, O.

(2019) Science 363:

Released	2018-12-05
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Danio rerio synthetic construct
Macromolecule	PDX1 C-terminal-inhibiting factor 1 (protein) m7G-capped RNA (nucleic acid)
Unique Ligands	B3P, EDO, M7G, SAH

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6QCV	Download File View File

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP

Cusack, S., Drncova, P.

(2019) Nat Struct Mol Biol 26: 460-470

Released	2019-06-05
Method	X-RAY DIFFRACTION 3.24 Å
Organisms	Influenza B virus (B/Memphis/13/2003) synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3
Unique Ligands	CTP, MG, PO4

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6QCW	Download File View File

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

Cusack, S., Drncova, P.

(2019) Nat Struct Mol Biol 26: 460-470

Released	2019-06-05
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Influenza B virus (B/Memphis/13/2003) synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3
Unique Ligands	PO4

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6QCX	Download File View File

Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer

Cusack, S., Drncova, P.

(2019) Nat Struct Mol Biol 26: 460-470

Released	2019-06-05
Method	X-RAY DIFFRACTION 3.08 Å
Organisms	Influenza B virus (B/Memphis/13/2003) synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3
Unique Ligands	MG, PO4, POP

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6RR7	Download File View File

Influenza A virus (A/NT/60/1968) polymerase Heterotrimer bound to 3'5' vRNA promoter and capped RNA primer

Carrique, L., Keown, J.R., Fan, H., Fodor, E., Grimes, J.M.

(2019) Nature 573: 287-290

Released	2019-09-04
Method	ELECTRON MICROSCOPY 3.01 Å
Organisms	Influenza A virus (A/nt/60/1968(H3N2)) Spodoptera frugiperda
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3

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6VU1	Download File View File

Cap3G-TAR-F1 is an RNA hairpin. The 1H-1H NOESY data was collected at 308 K in 10 mM KH2PO4 pH 7.4.

Summers, M.F., Brown, J.D.

(2020) Science 368: 413-417

Released	2020-04-29
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	RNA (34-MER) (nucleic acid)

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6VVJ	Download File View File

Cap1G-TPUA

Summers, M.F., Brown, J.D.

(2020) Science 368: 413-417

Released	2020-04-29
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	RNA (130-MER) (nucleic acid)

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6ZQG	Download File View File

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C

Cheng, J., Lau, B., Venuta, G.L., Berninghausen, O., Hurt, E., Beckmann, R.

(2020) Science 369: 1470-1476

Released	2020-09-23
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 33 Unique nucleic acid chains: 3
Unique Ligands	GTP, MG, ZN

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7JYY	Download File View File

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

(2021) Sci Signal 14:

Released	2020-09-16
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	2'-O-methyltransferase (protein) Non-structural protein 10 (protein) RNA (5'-D((M7G))-R(PAPUPUP*A)-3') (nucleic acid)
Unique Ligands	CL, FMT, MG, NA, SAM, ZN

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7JZ0	Download File View File

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

(2020) bioRxiv

Released	2020-09-16
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	2'-O-methyltransferase (protein) Non-structural protein 10 (protein) RNA (5'-D((M7G))-R(P(A2M)PUPU)-3') (nucleic acid)
Unique Ligands	CL, FMT, NA, SAH, ZN

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7L6R	Download File View File

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and Manganese (Mn).

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

(2021) Sci Signal 14:

Released	2021-01-06
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 synthetic construct
Macromolecule	2'-O-methyltransferase (protein) Non-structural protein 10 (protein) RNA (5'-D((M7G))-R(P(A2M)PUPUPAPA)-3') (nucleic acid)
Unique Ligands	BDF, CL, GLC, MN, SAH, SO4, ZN

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7L6T	Download File View File

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

(2021) Sci Signal 14:

Released	2021-01-06
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 synthetic construct
Macromolecule	2'-O-methyltransferase (protein) Non-structural protein 10 (protein) RNA (5'-D((M7G))-R(P(A2M)PUPUP*A)-3') (nucleic acid)
Unique Ligands	BDF, CL, FMT, GLC, MG, SAH, ZN

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8QOI	Download File View File

Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA

Holvec, S., Barchet, C., Frechin, L., Hazemann, I., von Loeffelholz, O., Klaholz, B.P.

(2024) Nat Struct Mol Biol 31: 1251-1264

Released	2024-06-12
Method	ELECTRON MICROSCOPY 1.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 75 Unique nucleic acid chains: 4
Unique Ligands	K, MG, SPD, ZN

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8R6W	Download File View File

Structure of the SFTSV L protein in a transcription-priming state with bound capped RNA [TRANSCRIPTION-PRIMING]

Williams, H.M., Thorkelsson, S.R., Vogel, D., Busch, C., Milewski, M., Cusack, S., Grunewald, K., Quemin, E.R.J., Rosenthal, M.

(2024) Nucleic Acids Res 52: 6049-6065

Released	2024-04-24
Method	ELECTRON MICROSCOPY 3.35 Å
Organisms	SFTS virus AH12
Macromolecule	RNA-directed RNA polymerase L (protein) RNA (5'-R((M7G)APAPA)-3') (nucleic acid) RNA (5'-R(APCPAPC)-3') (nucleic acid) RNA (5'-R(APCPAPCPAPGPAPGPAPCPGPCPCPCPAPG)-3') (nucleic acid) RNA (5'-R(PCPUPGPGPGPCPGPGPUPCPUPUPUPGPUPGP*U)-3') (nucleic acid)

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8R6Y	Download File View File

Structure of the SFTSV L protein stalled in a transcription-specific early elongation state with bound capped RNA [TRANSCRIPTION-EARLY-ELONGATION]

Williams, H.M., Thorkelsson, S.R., Vogel, D., Busch, C., Milewski, M., Cusack, S., Grunewald, K., Quemin, E.R.J., Rosenthal, M.

(2024) Nucleic Acids Res 52: 6049-6065

Released	2024-04-24
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	SFTS virus AH12
Macromolecule	RNA-directed RNA polymerase L (protein) RNA (5'-R((M7G)APAPA)-3') (nucleic acid) RNA (5'-R(APCPAPCPAPGPAPGPAPCPGPCPCPCPAPG)-3') (nucleic acid) RNA (5'-R(PAPCPA)-3') (nucleic acid) RNA (5'-R(PCPUPGPGPGPCPGPGPUPAPAPAPUPGPU)-3') (nucleic acid)
Unique Ligands	2KH, MG

1 to 18 of 18 Structures

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