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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:  download arrow rnaDB2003files.tgz (12.5MB)



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