The following table lists the RNA structural models used in our RNA backbone rotamer search. These files were selected from the Nucleic Acid Database with these filters:

• resolution 3.0A or better,
• no modifications to the sugar or phosphate,
• modified bases may be present, and
• where two or more files seemed to be essentially duplicate structures, the one with better resolution or R value was kept, though structures of portions of the ribosomal subunits at higher resolution than was available for the whole were kept in certain cases.

Proteins, DNA, waters, metals, and other groups not part of the RNA chain were eliminated, as were extra copies of the RNA within a file. The resulting coordinate files, with Reduce added hydrogens, are linked in the table. Clicking on the ID name will start a download of the zipped file. The database IDs are constructed from the NDB IDs:

• 'H' on the end designates that hydrogens have been added by Reduce,
• in cases where symmetry-related RNA chains have been removed from the RNAbb database coordinate files, we add the chain designation of the used, remaining chains in the ID name,
• IDs with no chain designations use all RNA chains available in the NDB coordinate file.

Structures pr0009 and pr0071 have also been edited to contain only one copy each of the elevenfold repeat.

Clicking on the linked ID will download the zip-compressed file. If you want all the files, then this g'zipped tarball is preferable:   rnaDB2003files.tgz (12.5MB)

RNAbb ID	PDB ID	SF's?	Reso.(Å)	# res	Name (** indicates no backbone clashes)
ar0001H	402D	Y	2.30	16	8-mer duplex
ar0002H	405D	Y	2.50	32	16-mer duplex
ar0004ABH	409D	NDB	2.50	16	8-mer duplex
ar0005H	413D		1.80	13	13-mer (one strand)
ar0006H	420D		1.90	32	16-mer duplex
ar0007H	422D	Y	2.60	24	12-mer duplex
ar0008H	433D	PDB	2.10	28	14-mer duplex
ar0009ABH	434D	PDB	1.16	14	**7-bp ala-tRNA acceptor stem
ar0011H	438D	PDB	2.50	18	**8-mer duplex
ar0012H	439D	Y	1.6	16	8-mer duplex (w/"wobble-like" G.C)
ar0013ABH	466D	Y	1.16	14	7-mer duplex from ala-tRNA of E. coli
ar0020ABH	1QCU	Y	1.20	22	**plasmid copy control
ar0021H	1QCO	Y	1.55	57	plasmid copy control
ar0022H	472D	Y	1.90	16	8-mer duplex (w/GG/UU)
ar0023H	1CSL	PDB	1.6	28	RRE high affinity site
ar0024ABH	1D4R	Y	2.00	58	fragment ofhuman SRP RNA helix 6
ar0027H	1DQH	Y	1.70	19	**Helix II of X. laevis somatic 5S RNA
ar0028ABH	1DUQ		2.10	22	rev. binding element of HIV-1
ar0030H	1G2J	Y	1.97	8	**8-mer with phenyl ribonucleotide
ar0032H	1I9X	Y	2.18	26	BPS-U2 snRNA duplex
ar0036H	1KD3	Y	1.80	22	11-mer duplex, thallium
ar0038H	1KD5	Y	1.58	22	**11-mer duplex, metal-free
ar0040H	1L3Z	Y	2.01	14	**7-mer duplex
ar0044H	1NLC	Y	1.85	46	HIV-1 DIS(MAL) genomic RNA
arb002H			0.8	4	**AU duplex
arb003ABH			1.1	4	**GC duplex - calcium
arb004H			0.89	4	**GC duplex - sodium
arb005H			0.85	4	**GC duplex - ammonium octahydrate
arf0108ABH	377D		1.76	12	6-mer duplex
arh064H	1RXB		1.80	16	**8-mer duplex
arh074H	259D		1.46	16	**8-mer duplex, hydration study
arl037H	255D		2.00	12	**one strand of duplex
arl048H	157D	Y	1.80	24	12-mer duplex
arl062ABH	1SDR		2.60	24	**E. coli Shine-Dalgarno seq
arn035H	1RNA		2.25	28	14-mer [U(U-A)6A]2
dr0005H	1F27		1.30	30	biotin-binding RNA pseudoknot
dr0008H	1MWL	Y	2.40	43	eubacterial 16S rRNA A site
dr0010H	1NTB	Y	2.90	40	streptomycin RNA-aptamer complex
drb002H			0.90	2	**AA + proflavine
drb003H			1.00	2	**AU + 9-aminoacridine
drb005H			0.8	2	**CA + proline
drb007H			1.34	4	**CG duplex + ethidium
drb008H			0.85	2	**CG + proflavin
drb018H			1.1	4	UA duplex + ethidium
drd004H			1.00	4	**CA/UG duplex + proflavine
pd0345RH	1MSW		2.10	10	RNA message, phage T7 RNA
pr0005BH	1DRZ		2.30	72	hepatitis delta virus genomic ribozyme
pr0006BH	1QF6	PDB	2.90	76	threonine tRNA from E. coli
pr0007MH	1CVJ		2.60	9	polyadenylate 9-mer (w/ poly(A)-bdg protein)
pr0008DEH	2A8V		2.40	9	RNA / rho transcription termination F
pr0009WH	1C9S	PDB	1.90	5	GAGAU-repeats / TRP RNA-bdg attenuation protein
pr0010BH	1CX0	PDB	2.30	72	hepatitis delta virus nested double pseudoknot
pr0011PH	1B7F		2.60	12	TRA pre-mRNA
pr0015CH	1QA6		2.80	58	1051-1108 from E. coli 23S rRNA
pr0017DEH	1DDL	Y	2.7	9	RNA from desmodium yellow mottle tymovirus
pr0018MNH	1DFU		1.80	38	loop E-helix IV fragments from 5S rRNA E. coli
pr0019BH	1C0A	PDB	2.40	76	asp-tRNA
pr0020CDH	1DI2	PDB	1.90	20	10-mer (w/dsRNA binding domain)
pr0021BH	1DUL		1.80	48	4.5S RNA domain IV
pr0022CH	1EC6		2.40	20	20-mer RNA hairpin
pr0026BH	1EUY	Y	2.60	75	gln-tRNA
pr0030BH	1F7U		2.2	76	arg-tRNA
pr0032TH	1FFY		2.2	74	ile-tRNA
pr0033BH	1FXL	Y	1.80	7	fragment of C-FOS AU-rich element
pr0034BH	1G2E	Y	2.30	10	fragment of AU-rich element of TNF alpha RNA
pr0036RH	1F8V		3.00	25	RNA from pariacoto virus
pr0037BH	1HQ1	Y	1.52	48	4.5S RNA domain 4 (res 32-74)
pr0040RSH	1E7X	Y	2.38	16	RNA hairpin (w/coat protein) from phage MS2
pr0046UH	1I5L	Y	2.75	3	UUU with snRNP SM-like protein AF-SM1
pr0047CH	1I6U	Y	2.60	37	16S rRNA fragment from M. jannaschii, with S8P
pr0051CFDH	1JBR	Y	2.15	62	ribotoxin and 31-mer SRD RNA inhibitor
pr0053CH	1JBT	Y	2.7	29	sarcin/ricin domain RNA analog
pr0055CH	1E7K		2.90	22	U4 snRNA
pr0057TH	1H4S	Y	2.85	66	pro-tRNA + tRNApro(CGG) from T. thermophilus
pr0060BH	1K8W	Y	1.85	22	T stem-loop RNA
pr0062RSH	1GKW	Y	2.56	26	MS2 RNA hairpin
pr0063ZH	1KNZ		2.45	5	rotavirus mRNA 3' consensus
pr0065RH	1KQ2	Y	2.71	7	RNA with host factor for Q beta
pr0067BH	1L9A		2.90	137	signal recognition particle RNA S domain
pr0069CH	1IVS		2.90	75	val-tRNA
pr0071WH	1GTF	Y	1.75	4	GAGUU repeat RNA with TRP-protein
pr0073BH	1LNG		2.30	97	7S.S SRP RNA
pr0075AH	1M50	Y	2.20	21	RNA hairpin ribozyme with U1A, STR virus
pr0078OPQRSTUH	1M8V	Y	2.60	41	uridine heptamer (with snRNP sm-like protein)
pr0079CDEFH	1M8W	Y	2.20	30	NRE1-19 RNA
pr0080CDH	1M8X	Y	2.20	15	NRE1-14 RNA
pr0081CH	1M8Y	Y	2.60	10	NRE2-10 RNA
pr0083CH	1MJI	Y	2.50	34	5S rRNA fragment
pr0085BH	1MZP	Y	2.65	55	23S rRNA fragment (L1 protuberance)
pr0090CH	1N78	Y	2.10	76	glu-tRNA
pr0091EH	1NB7		2.90	4	U-template for HC-JR RNA polymerase
prv001MH	1BMV	PDB	3.00	11	RNA in icosahedral virus (bountiful bean)
prv004NH	2BBV		2.80	10	RNA in black beetle virus
prv010RSH	6MSF	PDB	2.80	24	RNA in MS2
prv020BCDH	1A34	PDB	1.81	21	RNA in satellite tobacco mosaic virus
prv021RSH	1ZDJ	PDB	2.90	16	8-NT MS2 variant RNA fragment
pte003BH	1QTQ	Y	2.25	76	gln-tRNA
ptr004TH	1SER		2.90	66	ser-tRNA
ptr016QH	1A9N		2.38	24	U2 snRNA hairpin IV
rr0005BH	1DK1		2.80	52	rRNA fragment with S15 (30S)
rr0010BH	1F7Y		2.80	52	16S rRNA fragment (w/ UUCG tetraloops)
rr0016AXH	1FJG	PDB	3.00	1513	30S ribosomal subunit
rr0019DEH	1G1X		2.60	84	16S rRNA fragments
rr003309H	1JJ2	Y	2.40	2876	H. marismortui large ribosomal subunit
tr0001H	1EHZ	Y	1.93	76	phe-tRNA
trna12H	1YFG		3.00	76	yeast initiator tRNA
uh0001AH	1BR3		3.00	13	RNA complex with 10-23 DNA enzyme
uhx026AH	1HMH		2.60	34	hammerhead ribozyme (RNA-DNA) RNA strand
ur0001ABH	429D	Y	2.7	24	lead-dependent ribozyme
ur0004H	437D	Y	1.6	28	RNA pseudoknot from beet western yellow virus
ur0005H	462D	Y	2.30	46	HIV-1 genomic RNA dimerization initiation site
ur0007H	483D	Y	1.11	27	sarcin/ricin rRNA domain from E. coli
ur0009H	1DUH	Y	2.7	45	conserved domain IV of E. coli 4.5S RNA
ur0012AH	1HR2	Y	2.25	157	PR-P6 DELC209 mut, tetrahymena group I intron
ur0014H	1J8G		0.61	24	RNA tetraplex
ur0015H	1JJM	Y	2.60	46	HIV-1(LAI) genomic RNA 265-287
ur0019H	1KXK	Y	3.00	70	domains 5,6 of AI5G group II self-splicing intron
ur0020H	1L2X	Y	1.25	28	RNA pseudoknot, beet western yellow virus
ur0022AH	1L8V		2.80	157	P4-P6 RNA ribozyme domain group I intron
ur0026H	1MSY		1.41	27	**GUAA tetraloop mutant, sarcin/ricin from 23S
urb003H			1.00	2	**AA
urb008H			1.00	2	**UA
urb016H			0.86	4	**UA/UA
urc002H			0.95	3	**AAA
urf042H	1OSU	Y	1.40	6	**half of double helix, with UU overhang
url029H	205D		2.64	24	double helix with UU-pair in internal loop
url050ABH	280D	Y	2.40	24	RNA dodecamer w/internal loop
urt068AH	361D		3.00	20	domain E of Thermus flavus 5S rRNA, w/ tetraloop
urx053AH	1GID		2.50	158	P4-P6 ribozyme domain
urx059H	301D	Y	3.00	41	RNA hammerhead ribozyme
urx063H	353D		2.40	24	**Domain A of T. flavus 5S rRNA
urx075H	397D	Y	1.30	27	HIV-1 trans-activation response region