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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "PROTEIN/RNA"

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Search Summary

This query matches 974 Structures.

Refinements

Structure Determination Methodology

experimental (974)

Scientific Name of Source Organism

	Homo sapiens (272)
	synthetic construct (240)
	Escherichia coli (39)
	Mus musculus (32)
	Severe acute respiratory syndrome coronavirus 2 (29)
	Saccharomyces cerevisiae (27)
	Human immunodeficiency virus 1 (24)
	Caenorhabditis elegans (22)
	Saccharomyces cerevisiae S288C (22)
	Drosophila melanogaster (21)

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Taxonomy

	Eukaryota (457)
	Bacteria (301)
	other sequences (240)
	Riboviria (181)
	Archaea (47)
	unclassified sequences (32)
	Duplodnaviria (14)
	Riboviria (RNA viruses and viroids) (5)
	unclassified viruses (5)
	unclassified bacterial viruses (3)

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Experimental Method

	X-RAY DIFFRACTION (536)
	ELECTRON MICROSCOPY (362)
	SOLUTION NMR (76)

Polymer Entity Type

	Protein (973)
	RNA (919)
	DNA (108)
	NA-hybrid (24)

Refinement Resolution (Å)

	1.0 - 1.5 (23)
	1.5 - 2.0 (112)
	2.0 - 2.5 (140)
	2.5 - 3.0 (209)
	3.0 - 3.5 (261)
	3.5 - 4.0 (88)
	4.0 - 4.5 (21)
	> 4.5 (43)

Release Date

	1995 - 1999 (14)
	2000 - 2004 (37)
	2005 - 2009 (112)
	2010 - 2014 (199)
	2015 - 2019 (197)
	2020 - 2024 (376)
	2025 - 2029 (39)

Enzyme Classification Name

	Hydrolases (219)
	Transferases (92)
	Lyases (17)
	Isomerases (13)
	Ligases (8)

Symmetry Type

	Asymmetric (801)
	Cyclic (144)
	Dihedral (28)
	Helical (4)
	Icosahedral (3)
	Tetrahedral (3)

SCOP Classification

	Alpha and beta proteins (a+b) (104)
	All beta proteins (26)
	All alpha proteins (54)
	Artifacts (34)
	Alpha and beta proteins (a/b) (16)
	Small proteins (17)
	Peptides (12)
	Multi-domain proteins (alpha and beta) (4)
	Low resolution protein structures (6)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 974 Structures

Page 1 of 39

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2A8V \| pdb_00002a8v	Download File View File

RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX

Bogden, C.E., Fass, D., Bergman, N., Nichols, M.D., Berger, J.M.

(1999) Mol Cell 3: 487-493

Released	1999-04-26
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli Escherichia coli (strain K12)
Macromolecule	RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR (protein) 5'-R(PCPCPC)-3' (nucleic acid) 5'-R(PCPCPCPCPCP*C)-3' (nucleic acid)

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5LTA \| pdb_00005lta	Download File View File

Crystal structure of the Prp43-ADP-BeF3-U7-RNA complex

Tauchert, M.J., Ficner, R.

(2017) Elife 6:

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.621 Å
Organisms	Thermochaetoides thermophila DSM 1495 synthetic construct
Macromolecule	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (protein) RNA (5'-R(PUPUPUPUPUPUPUPU)-3') (nucleic acid)
Unique Ligands	ADP, BEF, CAC, MG

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8GXB \| pdb_00008gxb	Download File View File

Crystal structure of NAD+ -II riboswitch in complex with NAD+

Xu, X.C., Ren, A.M.

(2023) Nucleic Acids Res 51: 54-67

Released	2023-01-18
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens Streptococcus sp.
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) NAD+ II riboswitch (nucleic acid)
Unique Ligands	MG, NAD

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8GXC \| pdb_00008gxc	Download File View File

Crystal structure of NAD+ -II riboswitch in complex with NMN

Xu, X.C., Ren, A.M.

(2023) Nucleic Acids Res 51: 54-67

Released	2023-01-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Streptococcus sp.
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) 61-mer RNA (nucleic acid)
Unique Ligands	MG, NMN

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4GHA \| pdb_00004gha	Download File View File

Crystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA

Bale, S., Jean-Philippe, J., Bornholdt, Z.A., Kimberlin, C.K., Halfmann, P., Zandonatti, M.A., Kunert, J., Kroon, G.J.A., Kawaoka, Y., MacRae, I.J., Wilson, I.A., Saphire, E.O.

(2012) PLoS Pathog 8: e1002916-e1002916

Released	2012-08-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Marburg virus - Musoke, Kenya, 1980
Macromolecule	Polymerase cofactor VP35 (protein) RNA (5'-R(CPUPAPGPAPCPGPUPCPUPAPG)-3') (nucleic acid)

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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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1DUL \| pdb_00001dul	Download File View File

STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE

Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A.

(2000) Science 287: 1232-1239

Released	2000-02-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli synthetic construct
Macromolecule	Signal recognition particle protein (protein) 4.5 S RNA DOMAIN IV (nucleic acid)
Unique Ligands	K, MG

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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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1F6U \| pdb_00001f6u	Download File View File

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Chancellor, K.J., Summers, M.F.

(2000) J Mol Biology 301: 491-511

Released	2000-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 NUCLEOCAPSID PROTEIN (protein) HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING (nucleic acid)
Unique Ligands	ZN

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1FJE \| pdb_00001fje	Download File View File

SOLUTION STRUCTURE OF NUCLEOLIN RBD12 IN COMPLEX WITH SNRE RNA

Allain, F.H.T., Bouvet, P., Dieckmann, T., Feigon, J.

(2000) EMBO J 19: 6870-6881

Released	2001-01-03
Method	SOLUTION NMR
Organisms	Mesocricetus auratus
Macromolecule	NUCLEOLIN RBD12 (protein) SNRE 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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1HQ1 \| pdb_00001hq1	Download File View File

STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE

Batey, R.T., Sagar, M.B., Doudna, J.A.

(2001) J Mol Biology 307: 229-246

Released	2001-01-03
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Escherichia coli
Macromolecule	SIGNAL RECOGNITION PARTICLE PROTEIN (protein) 4.5S RNA DOMAIN IV (nucleic acid)
Unique Ligands	K, MG

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1JID \| pdb_00001jid	Download File View File

Human SRP19 in complex with helix 6 of Human SRP RNA

Wild, K., Sinning, I., Cusack, S.

(2001) Science 294: 598-601

Released	2001-10-19
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (protein) HELIX 6 OF HUMAN SRP RNA (nucleic acid)
Unique Ligands	MG

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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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1L9A \| pdb_00001l9a	Download File View File

CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA

Oubridge, C., Kuglstatter, A., Jovine, L., Nagai, K.

(2002) Mol Cell 9: 1251-1261

Released	2002-06-28
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (protein) signal recognition particle RNA S domain (nucleic acid)
Unique Ligands	MG, MMC

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1LNG \| pdb_00001lng	Download File View File

Crystal Structure of the SRP19-7S.S SRP RNA Complex of M. jannaschii

Hainzl, T., Huang, S., Sauer-Eriksson, A.E.

(2002) Nature 417: 767-771

Released	2002-06-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	Signal recognition particle 19 kDa protein (protein) 7S.S SRP RNA (nucleic acid)
Unique Ligands	MG

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1MFQ \| pdb_00001mfq	Download File View File

Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle

Kuglstatter, A., Oubridge, C., Nagai, K.

(2002) Nat Struct Biol 9: 740-744

Released	2002-09-20
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	signal recognition particle 19kDa protein (protein) signal recognition particle 54kDa protein (protein) 7S RNA of human SRP (nucleic acid)
Unique Ligands	CL, MG

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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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1QZW \| pdb_00001qzw	Download File View File

Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication

Rosendal, K.R., Wild, K., Montoya, G., Sinning, I.

(2003) Proc Natl Acad Sci U S A 100: 14701-14706

Released	2003-11-18
Method	X-RAY DIFFRACTION 4.1 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Signal recognition 54 kDa protein (protein) 7S 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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1RLG \| pdb_00001rlg	Download File View File

Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex

Moore, T., Zhang, Y., Fenley, M.O., Li, H.

(2004) Structure 12: 807-818

Released	2004-06-01
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	50S ribosomal protein L7Ae (protein) 25-MER (nucleic acid)

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1SDS \| pdb_00001sds	Download File View File

Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA

Hamma, T., Ferre-D'Amare, A.

(2004) Structure 12: 893-903

Released	2004-05-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	50S ribosomal protein L7Ae (protein) box H/ACA sRNA (nucleic acid)
Unique Ligands	CA, K

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1U6B \| pdb_00001u6b	Download File View File

CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS

Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.

(2004) Nature 430: 45-50

Released	2004-08-10
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) 197-MER (nucleic acid) 5'-R(APAPGPCPCPAPCPAPCPAPAPAPCPCPAPGPAPCPGP GPCPC)-3' (nucleic acid) 5'-R(CPAP*(5MU))-3' (nucleic acid)
Unique Ligands	K, MG

1 to 25 of 974 Structures

Page 1 of 39

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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

2A8V | pdb_00002a8v

5LTA | pdb_00005lta

8GXB | pdb_00008gxb

8GXC | pdb_00008gxc

4GHA | pdb_00004gha

1A1T | pdb_00001a1t

1BIV | pdb_00001biv

1DUL | pdb_00001dul

1ETF | pdb_00001etf

1ETG | pdb_00001etg

1F6U | pdb_00001f6u

1FJE | pdb_00001fje

1G70 | pdb_00001g70

1HQ1 | pdb_00001hq1

1JID | pdb_00001jid

1KNZ | pdb_00001knz

1L9A | pdb_00001l9a

1LNG | pdb_00001lng

1MFQ | pdb_00001mfq

1MNB | pdb_00001mnb

1QZW | pdb_00001qzw

1R9F | pdb_00001r9f

1RLG | pdb_00001rlg

1SDS | pdb_00001sds

1U6B | pdb_00001u6b