1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Comolli, L.R.
Ulyanov, N.B.
James, T.L.
Gmeiner, W.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
30
4371
4379
10.1093/nar/gkf560
12384583
NMR Structure of the 3' Stem-Loop from Human U4 snRNA
2002
10.2210/pdb1mfj/pdb
pdb_00001mfj
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3'stem-loop of human U4 snRNA
6422.879
5'-R(*GP*AP*CP*AP*GP*UP*CP*UP*CP*UP*AP*CP*GP*GP*AP*GP*AP*CP*UP*G)-3'
1
syn
polymer
no
no
GACAGUCUCUACGGAGACUG
GACAGUCUCUACGGAGACUG
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
46.208
A
2
A
1
-8.191
A_A2:G1_A
1
-31.163
-6.578
-1.033
-2.936
-17.006
1
19
A
3
A
20
-1.520
A_C3:G20_A
2
-0.918
-0.060
0.234
-0.113
-4.413
1
20
A
4
A
19
-4.577
A_A4:U19_A
3
-13.184
-0.021
0.090
-0.124
-6.629
1
19
A
5
A
18
-0.990
A_G5:C18_A
4
-19.337
0.053
0.040
-0.162
3.197
1
20
A
6
A
17
-4.386
A_U6:A17_A
5
-14.657
0.060
0.065
-0.134
12.561
1
19
A
7
A
16
-1.075
A_C7:G16_A
6
-13.527
-0.111
-0.158
-0.118
12.678
1
20
A
8
A
15
-1.356
A_U8:A15_A
7
-13.419
0.064
-0.457
-0.131
5.190
1
19
A
9
A
14
-4.391
A_C9:G14_A
8
20.834
0.043
-0.592
-0.276
7.233
2
A
10
A
13
-99.591
A_U10:G13_A
9
-13.174
0.898
-0.748
-5.524
-0.856
42.763
A
A
2
3
-14.048
A
A
1
20
2.952
-8.703
-3.683
-2.495
AA_A2C3:G20G1_AA
1
35.121
-56.692
23.183
-3.050
6.552
2.613
29.609
A
A
3
4
14.012
A
A
20
19
3.025
7.094
-0.416
-1.387
AA_C3A4:U19G20_AA
2
0.189
-0.374
28.764
-4.026
0.849
2.759
33.626
A
A
4
5
19.438
A
A
19
18
3.387
11.047
0.076
-1.407
AA_A4G5:C18U19_AA
3
0.306
-0.539
31.807
-4.179
-0.083
2.839
31.438
A
A
5
6
8.424
A
A
18
17
3.040
4.548
-0.213
-1.254
AA_G5U6:A17C18_AA
4
-1.250
2.315
31.091
-3.084
0.181
2.856
30.389
A
A
6
7
7.258
A
A
17
16
3.039
3.794
0.323
-1.394
AA_U6C7:G16A17_AA
5
1.044
-1.996
30.139
-3.349
-0.426
2.917
32.743
A
A
7
8
13.535
A
A
16
15
3.329
7.562
0.097
-1.455
AA_C7U8:A15G16_AA
6
1.543
-2.761
31.845
-3.844
0.086
2.390
34.539
A
A
8
9
30.045
A
A
15
14
3.725
17.080
-0.449
-1.848
AA_U8C9:G14A15_AA
7
-2.502
4.401
30.030
-5.769
0.367
2.595
90.132
A
A
9
10
7.383
A
A
14
13
2.822
10.353
-0.671
0.047
AA_C9U10:G13G14_AA
8
24.934
-17.781
86.836
-0.145
0.904
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-11-06
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2002-08-11
REL
REL
This sequence is part of human U4 snRNA.
sample
This structure was determined using
standard 2D homonuclear techniques
and complete relaxation matrix
analysis of NOE intensities.
Lowest total energy (a weighted sum of conformational energy and restraint energy).
15
10
2D NOESY
2D NOESY
DQF-COSY
2D TOCSY
natural abundance 13C-HMQC
10 mM sodium phosphate & 50 mM NaCl
6.4
ambient
303
K
10 mM sodium phosphate & 50 mM NaCl
6.4
ambient
293
K
Structures are based on 200 distance
restraints, of which 140 are quantitative
bounds for nonexchangeable protons
calculated with MARDIGRAS, 56 are upper
bounds for exchangeable protons, and
4 are hydrogen bond restraints.
complete relaxation matrix;
random error analysis of NOE;
torsion angle dynamics;
simulated annealing using Metropolis Monte Carlo;
restrained minimization
1
lowest total energy
1 mM RNA;
10 mM sodium phosphate buffer;
50 mM sodium chloride
D2O
1 mM RNA;
10 mM sodium phosphate buffer;
50 mM sodium chloride
90% H2O/10% D2O
Varian Associates, Inc.
collection
VNMR
6.1
Delaglio
processing
NMRPipe
2.1
Goddard & Kneller
data analysis
Sparky
3.0
Borgias et al.
iterative matrix relaxation
MARDIGRAS
3.2
Guentert
refinement
DYANA
1.5
Ulyanov et al.
refinement
miniCarlo
600
Varian
INOVA
G
1
n
1
G
1
A
A
2
n
2
A
2
A
C
3
n
3
C
3
A
A
4
n
4
A
4
A
G
5
n
5
G
5
A
U
6
n
6
U
6
A
C
7
n
7
C
7
A
U
8
n
8
U
8
A
C
9
n
9
C
9
A
U
10
n
10
U
10
A
A
11
n
11
A
11
A
C
12
n
12
C
12
A
G
13
n
13
G
13
A
G
14
n
14
G
14
A
A
15
n
15
A
15
A
G
16
n
16
G
16
A
A
17
n
17
A
17
A
C
18
n
18
C
18
A
U
19
n
19
U
19
A
G
20
n
20
G
20
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
7
5.61
0.80
101.50
107.11
A
A
A
C3'
C2'
C1'
A
A
A
15
15
15
N
3' Stem-Loop from Human U4 SNRNA
1
N
N
hydrog
G-A MISPAIR
A
G
1
A
N2
G
1
1_555
A
A
2
A
N7
A
2
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
20
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
A
4
A
N1
A
4
1_555
A
U
19
A
N3
U
19
1_555
hydrog
WATSON-CRICK
A
A
4
A
N6
A
4
1_555
A
U
19
A
O4
U
19
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
18
A
N3
C
18
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
18
A
O2
C
18
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
18
A
N4
C
18
1_555
hydrog
WATSON-CRICK
A
U
6
A
N3
U
6
1_555
A
A
17
A
N1
A
17
1_555
hydrog
WATSON-CRICK
A
U
6
A
O4
U
6
1_555
A
A
17
A
N6
A
17
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
A
A
15
A
N1
A
15
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
A
A
15
A
N6
A
15
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
A
G
14
A
N1
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
A
G
14
A
O6
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
A
G
14
A
N2
G
14
1_555
hydrog
U-G MISPAIR
A
U
10
A
O2
U
10
1_555
A
G
13
A
N1
G
13
1_555
hydrog
TYPE_28_PAIR
A
U
10
A
N3
U
10
1_555
A
G
14
A
O6
G
14
1_555
hydrog
TYPE_28_PAIR
A
U
10
A
O2
U
10
1_555
A
G
14
A
N1
G
14
1_555
RNA
RIBONUCLEIC ACID, RNA OLIGONUCLEOTIDE, STEM-AND-LOOP, U4 SMALL NUCLEAR RNA, UACG TETRALOOP, RNA
1MFJ
PDB
1
1MFJ
1
20
1MFJ
1
20
1MFJ
A
1
1
20
1
P 1