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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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

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Search Summary

This query matches 648 Structures.

Refinements

Structure Determination Methodology

experimental (648)

Scientific Name of Source Organism

	Homo sapiens (218)
	synthetic construct (181)
	Mus musculus (31)
	Saccharomyces cerevisiae (22)
	Caenorhabditis elegans (21)
	Saccharomyces cerevisiae S288C (20)
	Drosophila melanogaster (17)
	unidentified (13)
	Escherichia coli K-12 (12)
	Streptococcus pyogenes serotype M1 (12)

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Taxonomy

	Eukaryota (379)
	Bacteria (209)
	other sequences (181)
	Archaea (35)
	Riboviria (34)
	unclassified sequences (15)
	Duplodnaviria (14)
	Riboviria (RNA viruses and viroids) (3)
	Monodnaviria (2)
	unclassified viruses (2)

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Experimental Method

	X-RAY DIFFRACTION (377)
	ELECTRON MICROSCOPY (226)
	SOLUTION NMR (45)

Polymer Entity Type

	Protein (648)
	RNA (632)
	DNA (70)
	NA-hybrid (12)

Refinement Resolution (Å)

	1.0 - 1.5 (22)
	1.5 - 2.0 (89)
	2.0 - 2.5 (101)
	2.5 - 3.0 (132)
	3.0 - 3.5 (168)
	3.5 - 4.0 (64)
	4.0 - 4.5 (10)
	> 4.5 (17)

Release Date

	1995 - 1999 (7)
	2000 - 2004 (18)
	2005 - 2009 (38)
	2010 - 2014 (140)
	2015 - 2019 (161)
	2020 - 2024 (272)
	2025 - 2029 (12)

Enzyme Classification Name

	Hydrolases (142)
	Transferases (36)
	Lyases (11)
	Isomerases (10)
	Ligases (8)

Symmetry Type

	Asymmetric (551)
	Cyclic (88)
	Dihedral (17)
	Helical (1)

SCOP Classification

	All beta proteins (23)
	Alpha and beta proteins (a+b) (64)
	All alpha proteins (23)
	Alpha and beta proteins (a/b) (11)
	Artifacts (23)
	Small proteins (8)
	Peptides (4)
	Low resolution protein structures (5)
	Coiled coil proteins (1)
	Multi-domain proteins (alpha and beta) (1)

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1 to 25 of 648 Structures

Page 1 of 26

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1A9N \| pdb_00001a9n	Download File View File

CRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN COMPLEX BOUND TO A FRAGMENT OF U2 SMALL NUCLEAR RNA

Price, S.R., Evans, P.R., Nagai, K.

(1998) Nature 394: 645-650

Released	1998-09-23
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Homo sapiens
Macromolecule	SPLICEOSOMAL U2B'' (protein) U2A' (protein) RNA (5'-R(CPCPUPGPGPUPAPUPUPGPCPAPGPUPAPCPCPUPCPCPAPGP* GP*U)-3') (nucleic acid)

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1AUD \| pdb_00001aud	Download File View File

U1A-UTRRNA, NMR, 31 STRUCTURES

Allain, F.H.-T., Gubser, C.C., Howe, P.W.A., Nagai, K., Neuhaus, D., Varani, G.

(1997) EMBO J 16: 5764-5774

Released	1998-02-25
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	U1A 102 (protein) RNA 3UTR (nucleic acid)

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1B7F \| pdb_00001b7f	Download File View File

SXL-LETHAL PROTEIN/RNA COMPLEX

Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1999) Nature 398: 579-585

Released	1999-05-03
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Drosophila melanogaster
Macromolecule	PROTEIN (SXL-LETHAL PROTEIN) (protein) RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3') (nucleic acid)

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1C9S \| pdb_00001c9s	Download File View File

CRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PROTEIN WITH A 53-BASE SINGLE STRANDED RNA CONTAINING ELEVEN GAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES

Antson, A.A., Dodson, E.J., Dodson, G.G., Greaves, R.B., Chen, X.-P., Gollnick, P.

(1999) Nature 401: 235-242

Released	1999-09-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	TRP RNA-BINDING ATTENUATION PROTEIN (protein) SINGLE STRANDED RNA (55-MER) (nucleic acid)
Unique Ligands	TRP

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1DI2 \| pdb_00001di2	Download File View File

CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS

Ryter, J.M., Schultz, S.C.

(1998) EMBO J 17: 7505-7513

Released	1999-12-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Xenopus laevis
Macromolecule	DOUBLE STRANDED RNA BINDING PROTEIN A (protein) RNA (5'-R(GPGPCPGPCPGPCPGPCPC)-3') (nucleic acid)

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1DRZ \| pdb_00001drz	Download File View File

U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX

Ferre-D'Amare, A.R., Zhou, K., Doudna, J.A.

(1998) Nature 395: 567-574

Released	1999-02-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Hepatitis delta virus Homo sapiens
Macromolecule	PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A) (protein) RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME) (nucleic acid)
Unique Ligands	MG, SO4

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1EC6 \| pdb_00001ec6	Download File View File

CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOUND TO 20-MER RNA HAIRPIN

Lewis, H.A., Musunuru, K., Jensen, K.B., Edo, C., Chen, H.

(2000) Cell 100: 323-332

Released	2000-02-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	RNA-BINDING PROTEIN NOVA-2 (protein) 20-MER RNA HAIRPIN (nucleic acid)

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1EXY \| pdb_00001exy	Download File View File

SOLUTION STRUCTURE OF HTLV-1 PEPTIDE BOUND TO ITS RNA APTAMER TARGET

Jiang, F., Gorin, A., Hu, W., Majumdar, A., Baskerville, S., Xu, W., Ellington, A., Patel, D.J.

(1999) Structure 7: 1461-1472

Released	2000-05-15
Method	SOLUTION NMR
Organisms	Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A)
Macromolecule	HTLV-1 REX PEPTIDE (protein) RNA APTAMER, 33-MER (nucleic acid)

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1GTF \| pdb_00001gtf	Download File View File

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 53-nucleotide RNA molecule containing GAGUU repeats

Hopcroft, N.H., Wendt, A.L., Gollnick, P., Antson, A.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 615

Released	2002-04-05
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Geobacillus stearothermophilus synthetic construct
Macromolecule	TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) (protein) (GAGUU)10GAG 53-NUCLEOTIDE RNA (nucleic acid)
Unique Ligands	TRP

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1GTN \| pdb_00001gtn	Download File View File

Structure of the trp RNA-binding attenuation protein (TRAP) bound to an RNA molecule containing 11 GAGCC repeats

Hopcroft, N.H., Wendt, A.L., Gollnick, P., Antson, A.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 615

Released	2002-04-05
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	TRP RNA-BINDING ATTENUATION PROTEIN (protein) (GAGCC)11G 56-NUCLEOTIDE RNA (nucleic acid)
Unique Ligands	TRP

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1I5L \| pdb_00001i5l	Download File View File

CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA

Toro, I., Thore, S., Mayer, C., Basquin, J., Seraphin, B., Suck, D.

(2001) EMBO J 20: 2293-2303

Released	2001-08-28
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1 (protein) 5'-R(UPUP*U)-3' (nucleic acid)
Unique Ligands	URI

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1M8V \| pdb_00001m8v	Download File View File

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

Thore, S., Mayer, C., Sauter, C., Weeks, S., Suck, D.

(2003) J Biological Chem 278: 1239-1247

Released	2003-02-11
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus abyssi
Macromolecule	PUTATIVE SNRNP SM-LIKE PROTEIN (protein) 5'-R(PUPUPUPUPUPUP*U)-3' (nucleic acid)
Unique Ligands	CA, U5P

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1M8W \| pdb_00001m8w	Download File View File

CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-19 RNA

Wang, X., McLachlan, J., Zamore, P.D., Hall, T.M.T.

(2002) Cell 110: 501-512

Released	2002-09-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Pumilio 1 (protein) 5'-R(PUPGPUPAPUPAPU)-3' (nucleic acid) 5'-R(PUPGPUPCPCPAPG)-3' (nucleic acid) 5'-R(PUPUPGPUPAPUPAPU)-3' (nucleic acid) 5'-R(PUPUPGPUPCPCPAPG)-3' (nucleic acid)

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1M8X \| pdb_00001m8x	Download File View File

CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-14 RNA

Wang, X., McLachlan, J., Zamore, P.D., Hall, T.M.T.

(2002) Cell 110: 501-512

Released	2002-09-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Pumilio 1 (protein) 5'-R(PUPGPUPAPUPAPU)-3' (nucleic acid) 5'-R(PUPUPGPUPAPUPAP*U)-3' (nucleic acid)

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1M8Y \| pdb_00001m8y	Download File View File

CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE2-10 RNA

Wang, X., McLachlan, J., Zamore, P.D., Hall, T.M.T.

(2002) Cell 110: 501-512

Released	2002-09-25
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Pumilio 1 (protein) 5'-R(PAPUPUPGPUPAPCPAPUPA)-3' (nucleic acid)

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1P6V \| pdb_00001p6v	Download File View File

Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB

Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., Ban, N.

(2003) Nature 424: 699-703

Released	2003-08-12
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Aquifex aeolicus
Macromolecule	SsrA-binding protein (protein) 45-MER (nucleic acid)

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1PN7 \| pdb_00001pn7	Download File View File

Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome

Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.

(2003) Cell 114: 123-134

Released	2003-07-15
Method	ELECTRON MICROSCOPY 10.8 Å
Organisms	Thermotoga maritima Thermus thermophilus
Macromolecule	30S ribosomal protein S12 (protein) 50S ribosomal protein L11 (protein) P-tRNA (nucleic acid)

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1PN8 \| pdb_00001pn8	Download File View File

Coordinates of S12, L11 proteins and E-site tRNA from 70S crystal structure separately fitted into the Cryo-EM map of E.coli 70S.EF-G.GDPNP complex. The atomic coordinates originally from the E-site tRNA were fitted in the position of the hybrid P/E-site tRNA.

Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.

(2003) Cell 114: 123-134

Released	2003-07-15
Method	ELECTRON MICROSCOPY 10.8 Å
Organisms	Thermotoga maritima Thermus thermophilus
Macromolecule	30S ribosomal protein S12 (protein) 50S ribosomal protein L11 (protein) E-tRNA (nucleic acid)

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1QZC \| pdb_00001qzc	Download File View File

Coordinates of S12, SH44, LH69 and SRL separately fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Escherichia coli Thermus thermophilus
Macromolecule	30S ribosomal protein S12 (protein) 16S rRNA (nucleic acid) 23S rRNA (nucleic acid)

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1R2W \| pdb_00001r2w	Download File View File

Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of the 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Thermotoga maritima
Macromolecule	50S ribosomal protein L11 (protein) 58nts of 23S rRNA (nucleic acid)

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1R2X \| pdb_00001r2x	Download File View File

Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., Frank, J.

(2003) Nat Struct Biol 10: 899-906

Released	2003-11-04
Method	ELECTRON MICROSCOPY 9 Å
Organisms	Thermotoga maritima
Macromolecule	50S ribosomal protein L11 (protein) 58nts of 23S rRNA (nucleic acid)

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1RPU \| pdb_00001rpu	Download File View File

Crystal Structure of CIRV p19 bound to siRNA

Vargason, J.M., Szittya, G., Burgyan, J., Hall, T.M.T.

(2003) Cell 115: 799-811

Released	2004-01-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Carnation Italian ringspot virus
Macromolecule	19 kDa protein (protein) 5'-R(PCPGPUPAPCPGPCPGPUPCPAPCPGPCPGPUPAPCPGPUP*U)-3' (nucleic acid)

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1T4L \| pdb_00001t4l	Download File View File

Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with the 5' terminal RNA hairpin of snR47 precursor

Wu, H., Henras, A., Chanfreau, G., Feigon, J.

(2004) Proc Natl Acad Sci U S A 101: 8307-8312

Released	2004-06-01
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Ribonuclease III (protein) 5' terminal hairpin of snR47 precursor (nucleic acid)

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1UN6 \| pdb_00001un6	Download File View File

THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION

Lu, D., Searles, M.A., Klug, A.

(2003) Nature 426: 96

Released	2003-11-20
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Xenopus laevis
Macromolecule	TRANSCRIPTION FACTOR IIIA (protein) 5S RIBOSOMAL RNA (nucleic acid)
Unique Ligands	MG, ZN

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1YTU \| pdb_00001ytu	Download File View File

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

Ma, J.B., Yuan, Y.R., Meister, G., Pei, Y., Tuschl, T., Patel, D.J.

(2005) Nature 434: 666-670

Released	2005-04-05
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Archaeoglobus fulgidus DSM 4304
Macromolecule	hypothetical protein AF1318 (protein) 5'-R(PAPGPAPCPAPG)-3' (nucleic acid) 5'-R(PUPGPUPC)-3' (nucleic acid)
Unique Ligands	MG

1 to 25 of 648 Structures

Page 1 of 26

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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

1A9N | pdb_00001a9n

1AUD | pdb_00001aud

1B7F | pdb_00001b7f

1C9S | pdb_00001c9s

1DI2 | pdb_00001di2

1DRZ | pdb_00001drz

1EC6 | pdb_00001ec6

1EXY | pdb_00001exy

1GTF | pdb_00001gtf

1GTN | pdb_00001gtn

1I5L | pdb_00001i5l

1M8V | pdb_00001m8v

1M8W | pdb_00001m8w

1M8X | pdb_00001m8x

1M8Y | pdb_00001m8y

1P6V | pdb_00001p6v

1PN7 | pdb_00001pn7

1PN8 | pdb_00001pn8

1QZC | pdb_00001qzc

1R2W | pdb_00001r2w

1R2X | pdb_00001r2x

1RPU | pdb_00001rpu

1T4L | pdb_00001t4l

1UN6 | pdb_00001un6

1YTU | pdb_00001ytu