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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "Viral protein/RNA"

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Search Summary

This query matches 149 Structures.

Refinements

Structure Determination Methodology

experimental (149)

Scientific Name of Source Organism

	synthetic construct (31)
	Severe acute respiratory syndrome coronavirus 2 (29)
	Human immunodeficiency virus 1 (16)
	Homo sapiens (14)
	Escherichia coli (8)
	Vesicular stomatitis Indiana virus (8)
	Influenza D virus (D/swine/Oklahoma/1334/2011) (7)
	Human immunodeficiency virus type 1 BH10 (5)
	Moloney murine leukemia virus (5)
	Mammarenavirus machupoense (4)

More...

Taxonomy

	Riboviria (141)
	other sequences (31)
	Eukaryota (16)
	Bacteria (12)
	unclassified viruses (3)
	Riboviria (RNA viruses and viroids) (2)
	unclassified bacterial viruses (2)

Experimental Method

	ELECTRON MICROSCOPY (70)
	X-RAY DIFFRACTION (61)
	SOLUTION NMR (18)

Polymer Entity Type

	Protein (148)
	RNA (137)
	NA-hybrid (8)
	DNA (4)

Refinement Resolution (Å)

	1.5 - 2.0 (7)
	2.0 - 2.5 (16)
	2.5 - 3.0 (26)
	3.0 - 3.5 (47)
	3.5 - 4.0 (18)
	4.0 - 4.5 (8)
	> 4.5 (8)

Release Date

	1995 - 1999 (6)
	2000 - 2004 (5)
	2005 - 2009 (21)
	2010 - 2014 (29)
	2015 - 2019 (19)
	2020 - 2024 (65)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (52)
	Hydrolases (37)
	Lyases (6)

Symmetry Type

	Asymmetric (96)
	Cyclic (35)
	Dihedral (10)
	Helical (4)
	Icosahedral (3)

SCOP Classification

	All alpha proteins (7)
	Alpha and beta proteins (a+b) (10)
	Multi-domain proteins (alpha and beta) (1)
	Peptides (7)
	Artifacts (3)
	Small proteins (6)

AllSelected

1 to 25 of 149 Structures

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1A1T \| pdb_00001a1t	Download File View File

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES

De Guzman, R.N., Wu, Z.R., Stalling, C.C., Pappalardo, L., Borer, P.N., Summers, M.F.

(1998) Science 279: 384-388

Released	1998-06-17
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	NUCLEOCAPSID PROTEIN (protein) SL3 STEM-LOOP RNA (nucleic acid)
Unique Ligands	ZN

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1BIV \| pdb_00001biv	Download File View File

BOVINE IMMUNODEFICIENCY VIRUS TAT-TAR COMPLEX, NMR, 5 STRUCTURES

Ye, X., Kumar, R.A., Patel, D.J.

(1995) Chem Biol 2: 827-840

Released	1996-12-23
Method	SOLUTION NMR
Organisms	Bovine immunodeficiency virus synthetic construct
Macromolecule	TAT PEPTIDE (protein) TAR RNA (nucleic acid)

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1ETF \| pdb_00001etf	Download File View File

REV RESPONSE ELEMENT (RRE) RNA COMPLEXED WITH REV PEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE

Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Muhandiram, D.R., Kay, L.E., Frankel, A.D., Willamson, J.R.

(1996) Science 273: 1547-1551

Released	1997-03-12
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	REV PEPTIDE (protein) REV RESPONSE ELEMENT RNA (nucleic acid)

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1ETG \| pdb_00001etg	Download File View File

REV RESPONSE ELEMENT (RRE) RNA COMPLEXED WITH REV PEPTIDE, NMR, 19 STRUCTURES

Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Muhandiram, D.R., Kay, L.E., Frankel, A.D., Willamson, J.R.

(1996) Science 273: 1547-1551

Released	1997-03-12
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	REV PEPTIDE (protein) REV RESPONSIVE ELEMENT RNA (nucleic acid)

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1G70 \| pdb_00001g70	Download File View File

COMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE

Gosser, Y., Hermann, T., Majumdar, A., Hu, W., Frederick, R., Jiang, F., Xu, W., Patel, D.J.

(2001) Nat Struct Biol 8: 146-150

Released	2001-02-07
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	RSG-1.2 PEPTIDE (protein) HIV-1 RRE-IIB 32 NUCLEOTIDE RNA (nucleic acid)

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1KNZ \| pdb_00001knz	Download File View File

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer

Deo, R.C., Groft, C.M., Rajashankar, K.R., Burley, S.K.

(2002) Cell 108: 71-81

Released	2002-01-17
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Simian rotavirus A/SA11
Macromolecule	Nonstructural RNA-binding Protein 34 (protein) 5'-R(UPGPAPCP*C)-3' (nucleic acid)

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1MNB \| pdb_00001mnb	Download File View File

BIV TAT PEPTIDE (RESIDUES 68-81), NMR, MINIMIZED AVERAGE STRUCTURE

Puglisi, J.D., Chen, L., Blanchard, S., Frankel, A.D.

(1995) Science 270: 1200-1203

Released	1997-01-27
Method	SOLUTION NMR
Organisms	Bovine immunodeficiency virus (strain R29)
Macromolecule	BIV TAT PEPTIDE (protein) BIV TAR RNA (nucleic acid)

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1R9F \| pdb_00001r9f	Download File View File

Crystal structure of p19 complexed with 19-bp small interfering RNA

Ye, K., Malinina, L., Patel, D.J.

(2003) Nature 426: 874-878

Released	2004-01-27
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Tomato bushy stunt virus
Macromolecule	Core protein P19 (protein) 5'-R(CPGPUPAPCPGPCPGPGPAPAPUPAPCPUPUPCPGPAPUPU)-3' (nucleic acid) 5'-R(UPCPGPAPAPGPUPAPUPUPCPCPGPCPGPUPAPCPGPUPU)-3' (nucleic acid)
Unique Ligands	SO4

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1U6P \| pdb_00001u6p	Download File View File

NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein

D'Souza, V., Summers, M.F.

(2004) Nature 431: 586-590

Released	2004-11-02
Method	SOLUTION NMR
Organisms	Moloney murine leukemia virus
Macromolecule	Gag polyprotein (protein) 101-MER (nucleic acid)
Unique Ligands	ZN

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1ULL \| pdb_00001ull	Download File View File

RNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 STRUCTURES

Ye, X., Gorin, A., Ellington, A.D., Patel, D.J.

(1996) Nat Struct Biol 3: 1026-1033

Released	1997-08-20
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	REV PEPTIDE (protein) RNA (5'-R (GPGPCPUPGPGPAPCPUPCPGPUPAPCPUPUPCPGP GPUPAPCPUPGPGPAPGPAPAPAPCPAPGPCPC)-3') (nucleic acid)

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1WWD \| pdb_00001wwd	Download File View File

NMR structure determined for MLV NC complex with RNA sequence AACAGU

Dey, A., York, D., Smalls-Mantey, A., Summers, M.F.

(2005) Biochemistry 44: 3735-3744

Released	2005-03-22
Method	SOLUTION NMR
Organisms	Moloney murine leukemia virus
Macromolecule	Nucleoprotein p10 (protein) 5'-R(PAPAPCPAPGPU)-3' (nucleic acid)
Unique Ligands	ZN

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1WWE \| pdb_00001wwe	Download File View File

NMR Structure Determined for MLV NC complex with RNA Sequence UUUUGCU

Dey, A., York, D., Smalls-Mantey, A., Summers, M.F.

(2005) Biochemistry 44: 3735-3744

Released	2005-03-22
Method	SOLUTION NMR
Organisms	Moloney murine leukemia virus
Macromolecule	Nucleoprotein p10 (protein) 5'-R(PUPUPUPUPGPCP*U)-3' (nucleic acid)
Unique Ligands	ZN

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1WWF \| pdb_00001wwf	Download File View File

NMR Structure Determined for MLV NC Complex with RNA Sequence CCUCCGU

Dey, A., York, D., Smalls-Mantey, A., Summers, M.F.

(2005) Biochemistry 44: 3735-3744

Released	2005-04-05
Method	SOLUTION NMR
Organisms	Moloney murine leukemia virus
Macromolecule	Nucleoprotein p10 (protein) 5'-R(PCPCPUPCPCPGP*U)-3' (nucleic acid)
Unique Ligands	ZN

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1WWG \| pdb_00001wwg	Download File View File

NMR Structure Determined for MLV NC Complex with RNA Sequence UAUCUG

Dey, A., York, D., Smalls-Mantey, A., Summers, M.F.

(2005) Biochemistry 44: 3735-3744

Released	2005-04-05
Method	SOLUTION NMR
Organisms	Moloney murine leukemia virus
Macromolecule	Nucleoprotein p10 (protein) 5'-R(PUPAPUPCPUPG)-3' (nucleic acid)
Unique Ligands	ZN

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1XOK \| pdb_00001xok	Download File View File

crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N terminal peptide

Guogas, L.M., Filman, D.J., Hogle, J.M., Gehrke, L.

(2004) Science 306: 2108-2111

Released	2005-01-04
Method	X-RAY DIFFRACTION 3 Å
Organisms	Alfalfa mosaic virus (strain YSMV)
Macromolecule	Coat protein (protein) alfalfa mosaic virus RNA 3' UTR (nucleic acid)
Unique Ligands	BR

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2AZ0 \| pdb_00002az0	Download File View File

Flock House virus B2-dsRNA Complex (P212121)

Chao, J.A., Lee, J.H., Chapados, B.R., Debler, E.W., Schneemann, A., Williamson, J.R.

(2005) Nat Struct Mol Biol 12: 952-957

Released	2005-10-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Flock House virus
Macromolecule	B2 protein (protein) 5'-R(GPCPAP(5BU)PGPGPAPCPGPCPGP(5BU)PCPCPAP(5BU)PGPC)-3' (nucleic acid)

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2AZ2 \| pdb_00002az2	Download File View File

Flock House virus B2-dsRNA Complex (P4122)

Chao, J.A., Lee, J.H., Chapados, B.R., Debler, E.W., Schneemann, A., Williamson, J.R.

(2005) Nat Struct Mol Biol 12: 952-957

Released	2005-10-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Flock House virus
Macromolecule	B2 protein (protein) 5'-R(GPCPAP(5BU)PGPGPAPCPGPCPGP(5BU)PCPCPAP(5BU)PGPC)-3' (nucleic acid)

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2IHX \| pdb_00002ihx	Download File View File

Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:uPsi RNA Packaging Signal Complex

Zhou, J., Summers, M.

(2007) J Mol Biology 365: 453-467

Released	2007-01-16
Method	SOLUTION NMR
Organisms	Rous sarcoma virus
Macromolecule	Nucleocapsid (NC) Protein (protein) uPsi RNA (nucleic acid)
Unique Ligands	ZN

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2MQV \| pdb_00002mqv	Download File View File

Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein

D'Souza, V.M., Yildiz, Z.

(2014) Nature 515: 591-595

Released	2014-09-17
Method	SOLUTION NMR
Organisms	Murine leukemia virus
Macromolecule	Nucleocapsid protein p10 (protein) RNA (68-MER) (nucleic acid)
Unique Ligands	ZN

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2MS0 \| pdb_00002ms0	Download File View File

Solution NMR structure pf tRNApro:MLV-Nucleocapsid (1:2) Complex

D'Souza, V., Yildiz, Z.

(2014) Nature 515: 591-595

Released	2014-09-17
Method	SOLUTION NMR
Organisms	Murine leukemia virus
Macromolecule	Nucleocapsid protein p10 (protein) tRNApro (nucleic acid)
Unique Ligands	ZN

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2MS1 \| pdb_00002ms1	Download File View File

Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) Complex

D'Souza, V., Yildiz, Z.

(2014) Nature 515: 591-595

Released	2014-09-10
Method	SOLUTION NMR
Organisms	Murine leukemia virus
Macromolecule	Nucleocapsid protein p10 (protein) tRNApro (nucleic acid)
Unique Ligands	ZN

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2YHM \| pdb_00002yhm	Download File View File

Structure of respiratory syncytial virus nucleocapsid protein, P212121 crystal form

El Omari, K., Dhaliwal, B., Ren, J., Abrescia, N.G.A., Lockyer, M., Powell, K.L., Hawkins, A.R., Stammers, D.K.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1179

Released	2012-01-25
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Escherichia coli human respiratory syncytial virus
Macromolecule	NUCLEOPROTEIN (protein) RNA (nucleic acid)

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3CZ3 \| pdb_00003cz3	Download File View File

Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA

Ma, J.B., Li, F., Ding, S.W., Patel, D.J.

To be published

Released	2009-05-05
Method	X-RAY DIFFRACTION 3.23 Å
Organisms	Tomato aspermy virus
Macromolecule	Protein 2b (protein) RNA (5'-R(PCPGPUPAPCPGPCPGPGPAPAPUPAPCPUPUPCPGPA)-3') (nucleic acid) RNA (5'-R(PUPCPGPAPAPGPUPAPUPUPCPCPGPCPGPUPAPCPG)-3') (nucleic acid)

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3GPQ \| pdb_00003gpq	Download File View File

Crystal structure of macro domain of Chikungunya virus in complex with RNA

Malet, H., Jamal, S., Coutard, B., Canard, B.

(2009) J Virol 83: 6534-6545

Released	2009-07-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Chikungunya virus strain S27-African prototype
Macromolecule	Non-structural protein 3 (protein) RNA (5'-R(APAP*A)-3') (nucleic acid)

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3HHZ \| pdb_00003hhz	Download File View File

Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein

Green, T.J., Luo, M.

(2009) Proc Natl Acad Sci U S A 106: 11713-11718

Released	2009-07-28
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Escherichia coli Vesicular stomatitis Indiana virus
Macromolecule	Nucleoprotein (protein) Phosphoprotein (protein) RNA (45-MER) (nucleic acid)

1 to 25 of 149 Structures

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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

1A1T | pdb_00001a1t

1BIV | pdb_00001biv

1ETF | pdb_00001etf

1ETG | pdb_00001etg

1G70 | pdb_00001g70

1KNZ | pdb_00001knz

1MNB | pdb_00001mnb

1R9F | pdb_00001r9f

1U6P | pdb_00001u6p

1ULL | pdb_00001ull

1WWD | pdb_00001wwd

1WWE | pdb_00001wwe

1WWF | pdb_00001wwf

1WWG | pdb_00001wwg

1XOK | pdb_00001xok

2AZ0 | pdb_00002az0

2AZ2 | pdb_00002az2

2IHX | pdb_00002ihx

2MQV | pdb_00002mqv

2MS0 | pdb_00002ms0

2MS1 | pdb_00002ms1

2YHM | pdb_00002yhm

3CZ3 | pdb_00003cz3

3GPQ | pdb_00003gpq

3HHZ | pdb_00003hhz