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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:  download arrow rnaDB2005files.tgz (7MB)

For the list of RNA files in the updated version of the dataset, called RNA09, please download this list: &ndsp; download arrowRNA09 Final List (Excel worksheet). If you want the coordinate of all the files, please download this g'zipped tarball:   download arrow RNA09Files



RNAbb ID PDB ID Reso.(Å) # resids. Name
download arrowah0001Ha 404D
2.5
10
GAAGAGAAGC, double helix with DNA
download arrowah0005Hb 479D
1.9
9
GAAGAAGAG, double helix with DNA
download arrowah0010Hb 1EFO
2.3
10
GAAGAGAGAG, double helix with DNA
download arrowah0012Ha 1G4Q
1.15
9
CAAAGAAAG, double helix with DNA, mismatch
download arrowahh0114Ha 398D
1.94
8
GCAGUGGC
download arrowar0001H 402D
2.3
8
CGCCAGCG (dh)
download arrowar0002H 405D
2.5
32
GCAGACUUAAAUCUGC (dh)
download arrowar0004Hab 409D
2.5
16
CCCIUGGG (dh)
download arrowar0005H 413D
1.8
13
UGAGCUUCGGCUC (dh, one strand in asym. unit)
download arrowar0006H 420D
1.9
32
GCAGAGUUAAAUCUGC (dh)
download arrowar0007H 422D
2.6
24
GAUCACUUCGGU (dh)
download arrowar0008H 433D
2.1
28
GGUAUUGCGGUACC (dh)
download arrowar0009Hab 434D
1.16
14
UAGCUCC/GGGGCUA (dh, two copies)
download arrowar0011H 438D
2.5
18
GGGCGCUCC (dh)
download arrowar0012H 439D
1.6
16
CUGGGCGG/CCGCCUGG (dh)
download arrowar0013Hab 466D
1.16
14
UAGCUCC/GGGGCUA (dh)
download arrowar0021Hcd 1QC0
1.55
38
19bp plasmid copy control related dh
download arrowar0022H 472D
1.9
16
GUGUUUAC/GUAGGCAC (dh)
download arrowar0023H 1CSL
1.6
28
RRE high affinity rev binding site
download arrowar0024Hab 1D4R
2
29
29mer fragment of human SRP RNA helix 6
download arrowar0026H 1DQF
2.2
19
helix II of Xenopus laevis 5S rRNA (one form)
download arrowar0027H 1DQH
1.7
19
helix II of Xenopus laevis 5S rRNA (other form)
download arrowar0028Hab 1DUQ
2.1
24
rev binding element
download arrowar0030H 1G2J
1.97
7
CCC(PYY)GGGG (dh, one str. in asym. unit)
download arrowar0032H 1I9X
2.18
26
model branchpoint-U2 snRNA duplex w/bulge
download arrowar0035Hab 1JZV
1.7
17
bulge from SL2 stem-loop of psi-RNA
download arrowar0038H 1KD5
1.58
22
GGUCACAGCCC (dh), metal-free
download arrowar0040H 1L3Z
2.01
14
GUAUACA (dh)
download arrowar0041H 1LNT
1.7
24
conserved RNA internal loop of SRP
download arrowar0044H 1NLC
1.85
46
Zn-soaked
download arrowar0048Hab 1SA9
2.86
16
GGCGAGCC (dh); mult. Copies
download arrowar0049Hab 1SAQ
2.7
16
GICGAGCC (dh); mult. Copies
download arrowarb002H ----
0.8
4
AU (dh), Na salt
download arrowarb003Hab ----
1.1
4
GC (dh), Ca salt
download arrowarb004H ----
0.89
2
GC (dh), Na salt, one strand in asym. unit
download arrowarb005H ----
0.85
2
GC (dh), ammonium salt, one strand in asym. unit
download arrowarh074H 259D
1.46
16
CCCCGGGG (dh), rhombohedral re-refinement
download arrowarhb90H 333D
2.52
8
CGCAIGCG (dh, one strand in asym. unit)
download arrowarl037H 255D
2
12
GGACUUCGGUCC (dh, one strand in asym. unit)
download arrowarl048H 157D
1.8
24
CGCGAAUUAGCG (dh)
download arrowarl062Hab 1SDR
2.6
24
12mer containing E. coli Shine-Delgarno sequence
download arrowarn035H 1RNA
2.25
28
UUAUAUAUAUAUAA (dh)
download arrowdr0004Ha 1ET4
2.3
35
B12-binding aptamer with cobalamin
download arrowdr0005H 1F27
1.3
30
biotin-binding pseudoknot
download arrowdr0007H 1LC4
2.54
46
16S rRNA A site and tobramycin
download arrowdr0008H 1MWL
2.4
44
16S rRNA A site and geneticin
download arrowdr0010H 1NTB
2.9
40
streptomycin aptamer complex
download arrowdrb002H ----
0.9
2
AA/proflavine (not dh, one str. in asym. unit)
download arrowdrb003H ----
1
2
AU/9-aminoacridine (not dh, one str. in asym. unit)
download arrowdrb005H ----
0.8
2
CA (dh)/proflavine intercalated, one str. in asym. unit
download arrowdrb007H ----
1.34
4
CG (dh)/ethidium intercalated
download arrowdrb008H ----
0.85
2
CG (dh)/proflavine intercalated, one str. in asym. unit
download arrowdrb018H ----
1.1
4
UA (dh)/ethidium intercalated
download arrowdrd004H ----
1
4
CA/UG (dh)/proflavine
download arrowpd0345Hr 1MSW
2.1
10
DNA-directed RNA polymerase (RNA is chain R)
download arrowph0002Hr 1QLN
2.4
2
initiation complex of above?
download arrowph0003He 1HYS
3
23
reverse transcriptase, DNA/RNA (chain E)
download arrowph0009Hr 1S76
2.88
9
elongation complex; check chain R
download arrowpr0001Hrs 5MSF
2.8
36
CCGGAGGAUCACCACGGG
download arrowpr0002Hrs 7MSF
2.8
28
UCGCCAACAGGCGG
download arrowpr0006Hb 1QF6
2.9
90
thr-tRNA with cognate synthetase
download arrowpr0007Hm 1CVJ
2.6
11
poly-A binding protein and poly-A RNA
download arrowpr0008Hde 2A8V
2.4
9
rho transcription termination factor and RNA (D, E)
download arrowpr0009Hwpart 1C9S
1.9
5
trp RNA-binding attenuation protein (take ONE GAGAU repeat)
download arrowpr0010Hb 1CX0
2.3
72
U1A and HDV ribozyme
download arrowpr0011Hp 1B7F
2.6
12
sxl-lethal protein/rna complex
download arrowpr0017Hde 1DDL
2.7
9
UUUUUUU, UU
download arrowpr0018Hmn 1DFU
1.8
38
L25/5S:fragment
download arrowpr0019Hb 1C0A
2.4
77
asp-tRNA with synthetase and asp
download arrowpr0020Hcd 1DI2
1.9
20
DSRNA binding protein with GGCGCGCGCC (dh) (2 copies)
download arrowpr0022Hcd 1EC6
2.4
20
Nova-2 KH3 K-homology RBD and 20mer hairpin
download arrowpr0029Hc 1GAX
2.9
75
val-tRNA, synthetase, valyl-adenylate analogue
download arrowpr0030Hb 1F7U
2.2
76
arg-tRNA, synthetase, L-arg
download arrowpr0032Ht 1FFY
2.2
75
ile-tRNA with synthetase and mupirocin
download arrowpr0033Hb 1FXL
1.8
9
HuD and C-FOS RNA UUUUAUUUU
download arrowpr0034Hb 1G2E
2.3
10
HuD and tumor necrosis factor RNA UAUUUAUUUA
download arrowpr0036Hr 1F8V
3
25
pariacoto virus (chain R)
download arrowpr0037Hb 1HQ1
1.52
49
RNA with SRP fragment
download arrowpr0046Huy 1I5L
2.75
6
UUU with SM-like protein
download arrowpr0047Hc 1I6U
2.6
37
30S fragment and S8P
download arrowpr0049Hc 1IL2
2.6
75
asp-tRNA with E. coli synthetase
download arrowpr0051Hd 1JBR
2.15
31
restrictocin and 31mer SRD inhibitor (C, D, F)
download arrowpr0055Hc 1E7K
2.9
22
U4 snRNA fragment
download arrowpr0057Ht 1H4S
2.85
77
pro-tRNA, synthetase
download arrowpr0058Hd 1APG
3
2
AG in ricin
download arrowpr0059Hc 2FMT
2.8
78
met-tRNA, transferase, fmet
download arrowpr0060Hb 1K8W
1.85
22
T stem-loop RNA with psi55 pseudouridine synthase
download arrowpr0063Hz 1KNZ
2.45
5
UGACC (one of four copies)
download arrowpr0065Hr 1KQ2
2.71
7
AUUUUUG with host factor Q
download arrowpr0067Hb 1L9A
2.9
128
S domain of SRP with SRP19 protein
download arrowpr0071Hwpart 1GTF
1.75
5
trp RNA-binding attenuation protein (take ONE GAGUU repeat)
download arrowpr0072Hwpart 1GTN
2.5
5
trp RNA-binding attenuation protein (take ONE GAGCC repeat)
download arrowpr0073Hb 1LNG
2.3
111
SRP19-7S.S SRP RNA
download arrowpr0075Hab 1M5O
2.2
113
U1 snRNP/RNA inhibitor/RNA ribozyme
download arrowpr0078Ho 1M8V
2.6
7
UUUUUUU with SM protein (one copy of seven)
download arrowpr0080Hc 1M8X
2.2
8
NRE1-14 RNA with pumilio-homology domain
download arrowpr0081Hc 1M8Y
2.6
10
NRE2-10 RNA
download arrowpr0087Hbc 1N35
2.5
15
GGGGG, AUUAGCCCCC with pol lambda 3 from reovirus
download arrowpr0090Hc 1N78
2.1
75
glu-tRNA, synthetase, glutamol-AMP
download arrowpr0091He 1NB7
2.9
4
UUUU with HC-J4 polymerase
download arrowpr0092Hb 1J1U
1.95
77
tyr-tRNA, synthetase, L-tyr
download arrowpr0094Hc 1OOA
2.45
29
aptamer with NF-KB(P50)2 (or nuclear factor NF-kappa-B p105)
download arrowpr0099H3 1PGL
2.8
6
chain 3 (AGUCUC)
download arrowpr0100Hg 1PVO
3
2
UC rho termination factor
download arrowpr0101Hef 1Q2R
2.9
40
intermediate? With queuine tRNA-ribosyltransferase (check mod)
download arrowpr0105Hcde 1R3E
2.1
34
intermediate? With tRNA pseudouridine synthase (check for mod)
download arrowpr0106Hbc 1R9F
1.85
42?
P19 and 19bp siRNA
download arrowpr0107Hbcde 1RC7
2.15
20
GGCGCGCGCC (dh) with RNAase III complex
download arrowpr0108Hc 1RLG
2.7
25
SRNP initiation complex; box C/D
download arrowpr0109Hcd 1RPU
2.5
42
P19 and siRNA (see PR0104)
download arrowpr0111Ha 1S03
2.7
47
ribosomal protein S8 and SPC operon mRNA
download arrowpr0112Hb 1SI3
2.6
9
siRNA-like duplex with human domain; check for 1-5 connection?
download arrowpr0113Hd 1SDS
1.8
15
K-turn derived from archaeal box H/ACA SRNA with L7AE
download arrowpr0122Hr 1SJ3
2.2
76
HDV genomic precursor with Mg
download arrowpr0124Hc 1VFG
2.8
75
primer tRNA with tRNA nucleotidyl transferase
download arrowpr0128Hgj 1TFW
2.2
26
with tRNA nucleotidyltransferase, GHI and J longer, J diff.
download arrowpr0131Hcd 1WMQ
1.6
7
Hut operon positive regulatory protein/RNA complex
download arrowpr0134Hbc 1WNE
3
13
CAUGGGCC/GGCCC and FMV RNA-RNA polymerase
download arrowpr0135Ha 1U0B
2.3
74
cys-tRNA with synthetase
download arrowpr0141Hab 1XOK
3
39
RNA 3 - UTR with coat protein
download arrowpr0143He 1WSU
2.3
46
domain of elongation factor SelB
download arrowprv001Hm 1BMV
3
11
GGUCAAAAUGC
download arrowprv002Hp 1URN
1.92
21
RNA hairpin with U1A mutant, waters around P labeled chain U
download arrowprv004Hn 2BBV
2.8
10
UCUUAUAUCU
download arrowprv007Hb 1AV6
2.8
6
M7G-capped RNA hexamer with methyltransferase VP39
download arrowprv010Hrs 6MSF
2.8
24
F6 aptamer (2 chains) with MS2 coat protein
download arrowprv020Hbcd 1A34
1.81
21
AAAAAAAAAA/UUUUUUUUUUU with virus coat
download arrowprv021Hrs 1ZDJ
2.9
8
GGAUCACC (R, S) with coat
download arrowpte003Hb 1QTQ
2.25
75
gln-tRNA, synthetase, aa analog
download arrowptr004Ht 1SER
2.9
94
ser-tRNA, synthetase
download arrowptr016Hq 1A9N
2.38
24
fragment of U2 snRNA with U2B-U2A proteins
download arrowrr0005Hb 1DK1
2.8
57
fragment of 30S rRNA with S15
download arrowrr0009Hc 1MMS
2.57
58
fragment with L11
download arrowrr0012Hbc 1FEU
2.3
40
fragment of 5S, L25
download arrowrr0019Hde 1G1X
2.6
85
16S rRNA with S15, S6, S18
download arrowrr0082H09 1S72
2.4
3044
50S subunit, version 3
download arrowrr0096Hawx 1XMQ
3
1537
30S subunit with mRNA and perhaps lysine
download arrowtr0001H 1EHZ
1.93
76
phe-tRNA
download arrowtrna12H 1YFG
3
75
initiator tRNA (think this is Fmet)
download arrowuh0001Ha 1BR3
3
41
(chainA) Holliday junction formed by 10-23 DNA enzyme
download arrowuh0006Ha 1PJO
1.1
10
chainA, odd sugar conf., HIV-1 PPT hybrid
download arrowuhj055Ha 1FIX
2.3
10
chainA, substrate of ribonuclease activity of reverse transcriptase
download arrowuhx026Ha 1HMH
2.6
47
Hammerhead ribozyme w/DNA strand; use A/C/E (slight diff.)
download arrowur0009H 1DUH
2.7
45
domain IV of E. coli 4.5S rRNA (one strand in asym. unit)
download arrowur0012Ha 1HR2
2.25
158
P4-P6 domain of mutant Tetrahymena thermophila group I intron
download arrowur0014H 1J8G
0.61
24
UGGGGU tetraplex
download arrowur0015H 1JJM
2.6
46
dimerization initiation site(lai), kissing complexes
download arrowur0019H 1KXK
3
70
domain 5 and 6 of group II self-splicing intron
download arrowur0020H 1L2X
1.25
28
viral RNA pseudoknot
download arrowur0025H 1MHK
2.5
26
hook-turn (L and S different)
download arrowur0026H 1MSY
1.41
27
GUAA tetraloop mutant of sarcin/ricin domain
download arrowur0028Hab 1NUJ
1.8
24
leadzyme again
download arrowur0029H 1NYI
2.85
40
Crosslinked hammerhead ribozyme initial state
download arrowur0031H 1P79
1.1
6
UGUGGU bulged tetraplex
download arrowur0035H 1Q9A
1.04
27
sarcin/ricin domain from E. coli 23S rRNA
download arrowur0038H 1T0E
1.7
35
2-aminopurine-labeled decoding site RNA (ribosome fragment?)
download arrowur0039H 1U8D
1.95
68
guanine riboswitch with hypoxanthine
download arrowur0040H 1U9S
2.9
161
specificity domain of RNAse P, A-type
download arrowur0044H 1XJR
2.7
47
conserved element in SARS virus genome
download arrowur0051H 1Y26
2.1
71
A-riboswitch with adenine
download arrowur0052H 1Y27
2.4
68
G-riboswitch with guanine
download arrowurb003H ----
1
2
AA, hydrated calcium salt
download arrowurb008H ----
1
4
UA, two different conformations
download arrowurb016H ----
0.86
4
UA, two different conformations
download arrowurc002H ----
0.96
3
AAA (possibly with 132 intercalation)
download arrowurf042H 1OSU
1.4
6
UUCGCG (dh)
download arrowurl029H 205D
2.64
24
GGACUUUGGUCC (dh)
download arrowurl050Hab 280D
2.4
24
GGCGCUUGCGUC (dh)
download arrowurl051H 283D
2.3
12
GGCCGAAAGGCC (dh), one str. in asym. unit
download arrowurl064Ha 354D
1.5
24
loop E from E. coli 5S rRNA
download arrowurx063H 353D
2.4
24
domain A of T. flavus 5S rRNA
download arrowurx075H 397D
1.3
27
HIV-1 trans activation response region RNA stem