This table ("RNA05") is an updated version of the dataset of RNA structural models used in our initial RNA backbone rotamer search (Murray et al., 2003). Since the selection of the initial dataset in 2003, more structures have been determined, allowing us to add previously unavailable molecules and replace other structures with improved versions, increasing the total number of nucleotides from 8636 to 9486. The RNA05 dataset is the basis of a consensus list of backbone conformers (Richardson et al. publication submitted) developed by the ROC RNA Ontology Consortium.

These files were selected from the Nucleic Acid Database as of Feb. 2005 with these filters:

• resolution 3.0A or better,
• modified bases acceptable,
• modified sugar or phosphate ignored,
• selected among duplicate structures by resolution and R value, but retained higher-resolution structures of portions of the ribosomal subunits.

Hydrogens were added using Reduce. Proteins, DNA, waters, metals, and other non-RNA molecules were removed along with duplicate copies of the RNA within a file. The resulting 171 coordinate files are linked in the table below.

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.

Clicking on the linked ID will download the g'zip-compressed file. If you want all the files, then this g'zipped tarball is preferable:   rnaDB2005files.tgz (7MB)

RNAbb ID	PDB ID	Reso.(Å)	# resids.	Name
ah0001Ha	404D	2.5	10	GAAGAGAAGC, double helix with DNA
ah0005Hb	479D	1.9	9	GAAGAAGAG, double helix with DNA
ah0010Hb	1EFO	2.3	10	GAAGAGAGAG, double helix with DNA
ah0012Ha	1G4Q	1.15	9	CAAAGAAAG, double helix with DNA, mismatch
ahh0114Ha	398D	1.94	8	GCAGUGGC
ar0001H	402D	2.3	8	CGCCAGCG (dh)
ar0002H	405D	2.5	32	GCAGACUUAAAUCUGC (dh)
ar0004Hab	409D	2.5	16	CCCIUGGG (dh)
ar0005H	413D	1.8	13	UGAGCUUCGGCUC (dh, one strand in asym. unit)
ar0006H	420D	1.9	32	GCAGAGUUAAAUCUGC (dh)
ar0007H	422D	2.6	24	GAUCACUUCGGU (dh)
ar0008H	433D	2.1	28	GGUAUUGCGGUACC (dh)
ar0009Hab	434D	1.16	14	UAGCUCC/GGGGCUA (dh, two copies)
ar0011H	438D	2.5	18	GGGCGCUCC (dh)
ar0012H	439D	1.6	16	CUGGGCGG/CCGCCUGG (dh)
ar0013Hab	466D	1.16	14	UAGCUCC/GGGGCUA (dh)
ar0021Hcd	1QC0	1.55	38	19bp plasmid copy control related dh
ar0022H	472D	1.9	16	GUGUUUAC/GUAGGCAC (dh)
ar0023H	1CSL	1.6	28	RRE high affinity rev binding site
ar0024Hab	1D4R	2	29	29mer fragment of human SRP RNA helix 6
ar0026H	1DQF	2.2	19	helix II of Xenopus laevis 5S rRNA (one form)
ar0027H	1DQH	1.7	19	helix II of Xenopus laevis 5S rRNA (other form)
ar0028Hab	1DUQ	2.1	24	rev binding element
ar0030H	1G2J	1.97	7	CCC(PYY)GGGG (dh, one str. in asym. unit)
ar0032H	1I9X	2.18	26	model branchpoint-U2 snRNA duplex w/bulge
ar0035Hab	1JZV	1.7	17	bulge from SL2 stem-loop of psi-RNA
ar0038H	1KD5	1.58	22	GGUCACAGCCC (dh), metal-free
ar0040H	1L3Z	2.01	14	GUAUACA (dh)
ar0041H	1LNT	1.7	24	conserved RNA internal loop of SRP
ar0044H	1NLC	1.85	46	Zn-soaked
ar0048Hab	1SA9	2.86	16	GGCGAGCC (dh); mult. Copies
ar0049Hab	1SAQ	2.7	16	GICGAGCC (dh); mult. Copies
arb002H	----	0.8	4	AU (dh), Na salt
arb003Hab	----	1.1	4	GC (dh), Ca salt
arb004H	----	0.89	2	GC (dh), Na salt, one strand in asym. unit
arb005H	----	0.85	2	GC (dh), ammonium salt, one strand in asym. unit
arh074H	259D	1.46	16	CCCCGGGG (dh), rhombohedral re-refinement
arhb90H	333D	2.52	8	CGCAIGCG (dh, one strand in asym. unit)
arl037H	255D	2	12	GGACUUCGGUCC (dh, one strand in asym. unit)
arl048H	157D	1.8	24	CGCGAAUUAGCG (dh)
arl062Hab	1SDR	2.6	24	12mer containing E. coli Shine-Delgarno sequence
arn035H	1RNA	2.25	28	UUAUAUAUAUAUAA (dh)
dr0004Ha	1ET4	2.3	35	B12-binding aptamer with cobalamin
dr0005H	1F27	1.3	30	biotin-binding pseudoknot
dr0007H	1LC4	2.54	46	16S rRNA A site and tobramycin
dr0008H	1MWL	2.4	44	16S rRNA A site and geneticin
dr0010H	1NTB	2.9	40	streptomycin aptamer complex
drb002H	----	0.9	2	AA/proflavine (not dh, one str. in asym. unit)
drb003H	----	1	2	AU/9-aminoacridine (not dh, one str. in asym. unit)
drb005H	----	0.8	2	CA (dh)/proflavine intercalated, one str. in asym. unit
drb007H	----	1.34	4	CG (dh)/ethidium intercalated
drb008H	----	0.85	2	CG (dh)/proflavine intercalated, one str. in asym. unit
drb018H	----	1.1	4	UA (dh)/ethidium intercalated
drd004H	----	1	4	CA/UG (dh)/proflavine
pd0345Hr	1MSW	2.1	10	DNA-directed RNA polymerase (RNA is chain R)
ph0002Hr	1QLN	2.4	2	initiation complex of above?
ph0003He	1HYS	3	23	reverse transcriptase, DNA/RNA (chain E)
ph0009Hr	1S76	2.88	9	elongation complex; check chain R
pr0001Hrs	5MSF	2.8	36	CCGGAGGAUCACCACGGG
pr0002Hrs	7MSF	2.8	28	UCGCCAACAGGCGG
pr0006Hb	1QF6	2.9	90	thr-tRNA with cognate synthetase
pr0007Hm	1CVJ	2.6	11	poly-A binding protein and poly-A RNA
pr0008Hde	2A8V	2.4	9	rho transcription termination factor and RNA (D, E)
pr0009Hwpart	1C9S	1.9	5	trp RNA-binding attenuation protein (take ONE GAGAU repeat)
pr0010Hb	1CX0	2.3	72	U1A and HDV ribozyme
pr0011Hp	1B7F	2.6	12	sxl-lethal protein/rna complex
pr0017Hde	1DDL	2.7	9	UUUUUUU, UU
pr0018Hmn	1DFU	1.8	38	L25/5S:fragment
pr0019Hb	1C0A	2.4	77	asp-tRNA with synthetase and asp
pr0020Hcd	1DI2	1.9	20	DSRNA binding protein with GGCGCGCGCC (dh) (2 copies)
pr0022Hcd	1EC6	2.4	20	Nova-2 KH3 K-homology RBD and 20mer hairpin
pr0029Hc	1GAX	2.9	75	val-tRNA, synthetase, valyl-adenylate analogue
pr0030Hb	1F7U	2.2	76	arg-tRNA, synthetase, L-arg
pr0032Ht	1FFY	2.2	75	ile-tRNA with synthetase and mupirocin
pr0033Hb	1FXL	1.8	9	HuD and C-FOS RNA UUUUAUUUU
pr0034Hb	1G2E	2.3	10	HuD and tumor necrosis factor RNA UAUUUAUUUA
pr0036Hr	1F8V	3	25	pariacoto virus (chain R)
pr0037Hb	1HQ1	1.52	49	RNA with SRP fragment
pr0046Huy	1I5L	2.75	6	UUU with SM-like protein
pr0047Hc	1I6U	2.6	37	30S fragment and S8P
pr0049Hc	1IL2	2.6	75	asp-tRNA with E. coli synthetase
pr0051Hd	1JBR	2.15	31	restrictocin and 31mer SRD inhibitor (C, D, F)
pr0055Hc	1E7K	2.9	22	U4 snRNA fragment
pr0057Ht	1H4S	2.85	77	pro-tRNA, synthetase
pr0058Hd	1APG	3	2	AG in ricin
pr0059Hc	2FMT	2.8	78	met-tRNA, transferase, fmet
pr0060Hb	1K8W	1.85	22	T stem-loop RNA with psi55 pseudouridine synthase
pr0063Hz	1KNZ	2.45	5	UGACC (one of four copies)
pr0065Hr	1KQ2	2.71	7	AUUUUUG with host factor Q
pr0067Hb	1L9A	2.9	128	S domain of SRP with SRP19 protein
pr0071Hwpart	1GTF	1.75	5	trp RNA-binding attenuation protein (take ONE GAGUU repeat)
pr0072Hwpart	1GTN	2.5	5	trp RNA-binding attenuation protein (take ONE GAGCC repeat)
pr0073Hb	1LNG	2.3	111	SRP19-7S.S SRP RNA
pr0075Hab	1M5O	2.2	113	U1 snRNP/RNA inhibitor/RNA ribozyme
pr0078Ho	1M8V	2.6	7	UUUUUUU with SM protein (one copy of seven)
pr0080Hc	1M8X	2.2	8	NRE1-14 RNA with pumilio-homology domain
pr0081Hc	1M8Y	2.6	10	NRE2-10 RNA
pr0087Hbc	1N35	2.5	15	GGGGG, AUUAGCCCCC with pol lambda 3 from reovirus
pr0090Hc	1N78	2.1	75	glu-tRNA, synthetase, glutamol-AMP
pr0091He	1NB7	2.9	4	UUUU with HC-J4 polymerase
pr0092Hb	1J1U	1.95	77	tyr-tRNA, synthetase, L-tyr
pr0094Hc	1OOA	2.45	29	aptamer with NF-KB(P50)2 (or nuclear factor NF-kappa-B p105)
pr0099H3	1PGL	2.8	6	chain 3 (AGUCUC)
pr0100Hg	1PVO	3	2	UC rho termination factor
pr0101Hef	1Q2R	2.9	40	intermediate? With queuine tRNA-ribosyltransferase (check mod)
pr0105Hcde	1R3E	2.1	34	intermediate? With tRNA pseudouridine synthase (check for mod)
pr0106Hbc	1R9F	1.85	42?	P19 and 19bp siRNA
pr0107Hbcde	1RC7	2.15	20	GGCGCGCGCC (dh) with RNAase III complex
pr0108Hc	1RLG	2.7	25	SRNP initiation complex; box C/D
pr0109Hcd	1RPU	2.5	42	P19 and siRNA (see PR0104)
pr0111Ha	1S03	2.7	47	ribosomal protein S8 and SPC operon mRNA
pr0112Hb	1SI3	2.6	9	siRNA-like duplex with human domain; check for 1-5 connection?
pr0113Hd	1SDS	1.8	15	K-turn derived from archaeal box H/ACA SRNA with L7AE
pr0122Hr	1SJ3	2.2	76	HDV genomic precursor with Mg
pr0124Hc	1VFG	2.8	75	primer tRNA with tRNA nucleotidyl transferase
pr0128Hgj	1TFW	2.2	26	with tRNA nucleotidyltransferase, GHI and J longer, J diff.
pr0131Hcd	1WMQ	1.6	7	Hut operon positive regulatory protein/RNA complex
pr0134Hbc	1WNE	3	13	CAUGGGCC/GGCCC and FMV RNA-RNA polymerase
pr0135Ha	1U0B	2.3	74	cys-tRNA with synthetase
pr0141Hab	1XOK	3	39	RNA 3 - UTR with coat protein
pr0143He	1WSU	2.3	46	domain of elongation factor SelB
prv001Hm	1BMV	3	11	GGUCAAAAUGC
prv002Hp	1URN	1.92	21	RNA hairpin with U1A mutant, waters around P labeled chain U
prv004Hn	2BBV	2.8	10	UCUUAUAUCU
prv007Hb	1AV6	2.8	6	M7G-capped RNA hexamer with methyltransferase VP39
prv010Hrs	6MSF	2.8	24	F6 aptamer (2 chains) with MS2 coat protein
prv020Hbcd	1A34	1.81	21	AAAAAAAAAA/UUUUUUUUUUU with virus coat
prv021Hrs	1ZDJ	2.9	8	GGAUCACC (R, S) with coat
pte003Hb	1QTQ	2.25	75	gln-tRNA, synthetase, aa analog
ptr004Ht	1SER	2.9	94	ser-tRNA, synthetase
ptr016Hq	1A9N	2.38	24	fragment of U2 snRNA with U2B-U2A proteins
rr0005Hb	1DK1	2.8	57	fragment of 30S rRNA with S15
rr0009Hc	1MMS	2.57	58	fragment with L11
rr0012Hbc	1FEU	2.3	40	fragment of 5S, L25
rr0019Hde	1G1X	2.6	85	16S rRNA with S15, S6, S18
rr0082H09	1S72	2.4	3044	50S subunit, version 3
rr0096Hawx	1XMQ	3	1537	30S subunit with mRNA and perhaps lysine
tr0001H	1EHZ	1.93	76	phe-tRNA
trna12H	1YFG	3	75	initiator tRNA (think this is Fmet)
uh0001Ha	1BR3	3	41	(chainA) Holliday junction formed by 10-23 DNA enzyme
uh0006Ha	1PJO	1.1	10	chainA, odd sugar conf., HIV-1 PPT hybrid
uhj055Ha	1FIX	2.3	10	chainA, substrate of ribonuclease activity of reverse transcriptase
uhx026Ha	1HMH	2.6	47	Hammerhead ribozyme w/DNA strand; use A/C/E (slight diff.)
ur0009H	1DUH	2.7	45	domain IV of E. coli 4.5S rRNA (one strand in asym. unit)
ur0012Ha	1HR2	2.25	158	P4-P6 domain of mutant Tetrahymena thermophila group I intron
ur0014H	1J8G	0.61	24	UGGGGU tetraplex
ur0015H	1JJM	2.6	46	dimerization initiation site(lai), kissing complexes
ur0019H	1KXK	3	70	domain 5 and 6 of group II self-splicing intron
ur0020H	1L2X	1.25	28	viral RNA pseudoknot
ur0025H	1MHK	2.5	26	hook-turn (L and S different)
ur0026H	1MSY	1.41	27	GUAA tetraloop mutant of sarcin/ricin domain
ur0028Hab	1NUJ	1.8	24	leadzyme again
ur0029H	1NYI	2.85	40	Crosslinked hammerhead ribozyme initial state
ur0031H	1P79	1.1	6	UGUGGU bulged tetraplex
ur0035H	1Q9A	1.04	27	sarcin/ricin domain from E. coli 23S rRNA
ur0038H	1T0E	1.7	35	2-aminopurine-labeled decoding site RNA (ribosome fragment?)
ur0039H	1U8D	1.95	68	guanine riboswitch with hypoxanthine
ur0040H	1U9S	2.9	161	specificity domain of RNAse P, A-type
ur0044H	1XJR	2.7	47	conserved element in SARS virus genome
ur0051H	1Y26	2.1	71	A-riboswitch with adenine
ur0052H	1Y27	2.4	68	G-riboswitch with guanine
urb003H	----	1	2	AA, hydrated calcium salt
urb008H	----	1	4	UA, two different conformations
urb016H	----	0.86	4	UA, two different conformations
urc002H	----	0.96	3	AAA (possibly with 132 intercalation)
urf042H	1OSU	1.4	6	UUCGCG (dh)
url029H	205D	2.64	24	GGACUUUGGUCC (dh)
url050Hab	280D	2.4	24	GGCGCUUGCGUC (dh)
url051H	283D	2.3	12	GGCCGAAAGGCC (dh), one str. in asym. unit
url064Ha	354D	1.5	24	loop E from E. coli 5S rRNA
urx063H	353D	2.4	24	domain A of T. flavus 5S rRNA
urx075H	397D	1.3	27	HIV-1 trans activation response region RNA stem