1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Wang, Z.
Feigon, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
425
546
562
10.1016/j.jmb.2012.11.025
23201338
Intrinsic Dynamics of an Extended Hydrophobic Core in the S. cerevisiae RNase III dsRBD Contributes to Recognition of Specific RNA Binding Sites.
2013
UK
Structure
STRUE6
2005
0969-2126
19
999
1010
10.1016/j.str.2011.03.022
21742266
Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs.
2011
10.2210/pdb2luq/pdb
pdb_00002luq
9822.364
Ribonuclease 3
1
man
polymer
Ribonuclease III, RNase III
no
no
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAK
QRAAIPRSES
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAK
QRAAIPRSES
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Baker's yeast
ATCC 204508 / S288c
sample
RNT1, YM9408.01C, YM9959.21, YMR239C
559292
Saccharomyces cerevisiae
YMR239C
511693
Escherichia coli
BL21
plasmid
PGEX-2T
database_2
pdbx_database_status
pdbx_nmr_software
struct_ref_seq_dif
repository
Initial release
Database references
Database references
Data collection
Database references
Other
1
0
2012-12-05
1
1
2012-12-19
1
2
2013-02-13
1
3
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
BMRB
Y
RCSB
2012-06-19
REL
REL
REL
REL
1859
585
410
420
444
structures with the lowest energy
100
20
2D 1H-15N HSQC
3D HNCACB
3D CBCA(CO)NH
3D HNCO
3D HCCH-TOCSY
3D HCCH-COSY
3D 1H-15N NOESY
3D 1H-13C NOESY aliphatic
1
mM
[U-100% 13C; U-100% 15N]
90
%
10
%
[U-100% 2H]
150
mM
20
mM
1
mM
[U-100% 13C; U-100% 15N]
100
%
[U-100% 2H]
150
%
20
mM
150
6.5
ambient
298
K
simulated annealing
1
lowest energy
1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 150 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O
90% H2O/10% D2O
1 mM [U-100% 13C; U-100% 15N] protein, 100 % [U-100% 2H] D2O, 150 % sodium chloride, 20 mM sodium phosphate, 100% D2O
100% D2O
Bruker Biospin
collection
TopSpin
2.0
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Johnson, One Moon Scientific
chemical shift assignment
NMRView
Cornilescu, Delaglio and Bax
data analysis
TALOS
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
500
Bruker
DRX
Bruker DRX
600
Bruker
DRX
Bruker DRX
GLY
364
n
1
GLY
364
A
SER
365
n
2
SER
365
A
LEU
366
n
3
LEU
366
A
ASP
367
n
4
ASP
367
A
MET
368
n
5
MET
368
A
ASN
369
n
6
ASN
369
A
ALA
370
n
7
ALA
370
A
LYS
371
n
8
LYS
371
A
ARG
372
n
9
ARG
372
A
GLN
373
n
10
GLN
373
A
LEU
374
n
11
LEU
374
A
TYR
375
n
12
TYR
375
A
SER
376
n
13
SER
376
A
LEU
377
n
14
LEU
377
A
ILE
378
n
15
ILE
378
A
GLY
379
n
16
GLY
379
A
TYR
380
n
17
TYR
380
A
ALA
381
n
18
ALA
381
A
SER
382
n
19
SER
382
A
LEU
383
n
20
LEU
383
A
ARG
384
n
21
ARG
384
A
LEU
385
n
22
LEU
385
A
HIS
386
n
23
HIS
386
A
TYR
387
n
24
TYR
387
A
VAL
388
n
25
VAL
388
A
THR
389
n
26
THR
389
A
VAL
390
n
27
VAL
390
A
LYS
391
n
28
LYS
391
A
LYS
392
n
29
LYS
392
A
PRO
393
n
30
PRO
393
A
THR
394
n
31
THR
394
A
ALA
395
n
32
ALA
395
A
VAL
396
n
33
VAL
396
A
ASP
397
n
34
ASP
397
A
PRO
398
n
35
PRO
398
A
ASN
399
n
36
ASN
399
A
SER
400
n
37
SER
400
A
ILE
401
n
38
ILE
401
A
VAL
402
n
39
VAL
402
A
GLU
403
n
40
GLU
403
A
CYS
404
n
41
CYS
404
A
ARG
405
n
42
ARG
405
A
VAL
406
n
43
VAL
406
A
GLY
407
n
44
GLY
407
A
ASP
408
n
45
ASP
408
A
GLY
409
n
46
GLY
409
A
THR
410
n
47
THR
410
A
VAL
411
n
48
VAL
411
A
LEU
412
n
49
LEU
412
A
GLY
413
n
50
GLY
413
A
THR
414
n
51
THR
414
A
GLY
415
n
52
GLY
415
A
VAL
416
n
53
VAL
416
A
GLY
417
n
54
GLY
417
A
ARG
418
n
55
ARG
418
A
ASN
419
n
56
ASN
419
A
ILE
420
n
57
ILE
420
A
LYS
421
n
58
LYS
421
A
ILE
422
n
59
ILE
422
A
ALA
423
n
60
ALA
423
A
GLY
424
n
61
GLY
424
A
ILE
425
n
62
ILE
425
A
ARG
426
n
63
ARG
426
A
ALA
427
n
64
ALA
427
A
ALA
428
n
65
ALA
428
A
GLU
429
n
66
GLU
429
A
ASN
430
n
67
ASN
430
A
ALA
431
n
68
ALA
431
A
LEU
432
n
69
LEU
432
A
ARG
433
n
70
ARG
433
A
ASP
434
n
71
ASP
434
A
LYS
435
n
72
LYS
435
A
LYS
436
n
73
LYS
436
A
MET
437
n
74
MET
437
A
LEU
438
n
75
LEU
438
A
ASP
439
n
76
ASP
439
A
PHE
440
n
77
PHE
440
A
TYR
441
n
78
TYR
441
A
ALA
442
n
79
ALA
442
A
LYS
443
n
80
LYS
443
A
GLN
444
n
81
GLN
444
A
ARG
445
n
82
ARG
445
A
ALA
446
n
83
ALA
446
A
ALA
447
n
84
ALA
447
A
ILE
448
n
85
ILE
448
A
PRO
449
n
86
PRO
449
A
ARG
450
n
87
ARG
450
A
SER
451
n
88
SER
451
A
GLU
452
n
89
GLU
452
A
SER
453
n
90
SER
453
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
A
N
HIS
386
A
N
HIS
23
A
O
ARG
405
A
O
ARG
42
A
N
CYS
404
A
N
CYS
41
A
O
LEU
412
A
O
LEU
49
1
A
A
O
H
LYS
ILE
421
425
1.47
1
A
A
O
H
VAL
GLY
406
409
1.58
2
A
A
O
H
LYS
ILE
421
425
1.49
2
A
A
O
H
VAL
GLY
406
409
1.53
2
A
A
O
H
GLU
ARG
429
433
1.56
3
A
A
O
H
LYS
ILE
421
425
1.46
3
A
A
O
H
GLU
ARG
429
433
1.50
3
A
A
O
H
VAL
GLY
406
409
1.56
4
A
A
O
H
GLU
ARG
429
433
1.44
4
A
A
O
H
LYS
ILE
421
425
1.51
4
A
A
O
H
VAL
GLY
406
409
1.57
5
A
A
O
H
LYS
ILE
421
425
1.46
5
A
A
O
H
VAL
GLY
406
409
1.56
6
A
A
O
H
LYS
ILE
421
425
1.48
6
A
A
O
H
VAL
GLY
406
409
1.56
6
A
A
O
H
GLU
ARG
429
433
1.56
7
A
A
O
H
LYS
ILE
421
425
1.48
7
A
A
O
H
GLU
ARG
429
433
1.49
7
A
A
O
H
VAL
GLY
406
409
1.54
8
A
A
O
H
GLU
ARG
429
433
1.44
8
A
A
O
H
LYS
ILE
421
425
1.48
8
A
A
O
H
VAL
GLY
406
409
1.57
8
A
A
O
HG
LYS
SER
391
400
1.59
9
A
A
O
H
LYS
ILE
421
425
1.50
9
A
A
O
H
VAL
GLY
406
409
1.55
9
A
A
O
H
GLU
ARG
429
433
1.58
10
A
A
O
H
GLU
ARG
429
433
1.44
10
A
A
O
H
LYS
ILE
421
425
1.49
10
A
A
O
HG
LYS
SER
391
400
1.54
10
A
A
O
H
VAL
GLY
406
409
1.55
11
A
A
O
H
LYS
ILE
421
425
1.48
11
A
A
O
H
GLU
ARG
429
433
1.48
11
A
A
O
H
LEU
GLY
383
407
1.55
11
A
A
O
HG
LYS
SER
391
400
1.56
11
A
A
O
H
VAL
GLY
406
409
1.58
12
A
A
O
H
GLU
ARG
429
433
1.45
12
A
A
O
H
LYS
ILE
421
425
1.46
12
A
A
O
H
VAL
GLY
406
409
1.51
13
A
A
O
H
LYS
ILE
421
425
1.44
13
A
A
O
H
VAL
GLY
406
409
1.53
13
A
A
O
H
GLU
ARG
429
433
1.58
14
A
A
O
H
GLU
ARG
429
433
1.44
14
A
A
O
H
VAL
GLY
406
409
1.53
14
A
A
O
H
LYS
ILE
421
425
1.54
15
A
A
O
H
LYS
ILE
421
425
1.52
15
A
A
O
H
VAL
GLY
406
409
1.58
15
A
A
O
H
GLU
ARG
429
433
1.59
16
A
A
O
H
LYS
ILE
421
425
1.51
16
A
A
O
H
GLU
ARG
429
433
1.52
16
A
A
O
H
LEU
GLY
383
407
1.58
16
A
A
O
H
VAL
GLY
406
409
1.58
17
A
A
O
H
LYS
ILE
421
425
1.46
17
A
A
O
H
GLU
ARG
429
433
1.55
17
A
A
O
H
VAL
GLY
406
409
1.56
18
A
A
O
H
GLU
ARG
429
433
1.46
18
A
A
O
H
LYS
ILE
421
425
1.46
18
A
A
O
H
VAL
GLY
406
409
1.56
19
A
A
O
H
LYS
ILE
421
425
1.49
19
A
A
O
H
LEU
GLY
383
407
1.56
20
A
A
O
H
LYS
ILE
421
425
1.47
20
A
A
O
H
ILE
GLY
420
424
1.51
20
A
A
O
H
VAL
GLY
406
409
1.52
1
A
ARG
384
30.74
46.33
1
A
PRO
398
-78.00
42.56
1
A
THR
414
-162.04
115.74
1
A
ALA
447
-87.80
32.92
2
A
SER
365
64.71
151.47
2
A
TYR
380
-174.41
129.81
2
A
ARG
384
30.32
48.09
2
A
PRO
398
-79.48
45.69
2
A
VAL
411
-55.93
99.55
2
A
ALA
447
-89.18
32.78
2
A
ILE
448
-33.72
123.38
2
A
ARG
450
-91.38
-155.24
2
A
SER
451
52.67
91.88
3
A
ARG
384
30.69
51.93
3
A
PRO
398
-81.79
48.68
3
A
ALA
447
-90.67
33.16
3
A
SER
451
-165.37
62.18
3
A
GLU
452
62.46
-88.04
4
A
SER
365
165.55
-60.36
4
A
ARG
384
23.94
61.93
4
A
PRO
398
-79.80
44.38
4
A
ALA
447
-93.84
32.40
4
A
ILE
448
-43.20
102.94
5
A
ASP
367
-55.66
-171.11
5
A
ARG
384
25.04
62.07
5
A
PRO
398
-75.79
49.93
5
A
ALA
447
-95.61
32.29
5
A
SER
451
177.13
-53.40
5
A
GLU
452
79.37
-58.98
6
A
LEU
383
-97.82
40.53
6
A
ARG
384
-56.30
79.01
6
A
PRO
398
-69.48
50.24
6
A
ALA
447
-88.01
33.43
6
A
PRO
449
-75.83
48.91
6
A
ARG
450
66.84
134.18
7
A
LEU
383
-89.74
40.64
7
A
ARG
384
-40.05
83.83
7
A
PRO
398
-80.12
43.94
7
A
ALA
447
-87.20
32.83
7
A
ILE
448
-33.11
128.54
7
A
ARG
450
170.60
-86.33
7
A
SER
451
64.67
92.66
7
A
GLU
452
-154.80
-40.45
8
A
SER
365
65.23
104.26
8
A
ASP
367
-56.01
-175.84
8
A
ARG
384
30.11
83.32
8
A
PRO
398
-80.19
45.66
8
A
ALA
447
-88.29
33.10
8
A
ILE
448
-33.02
95.17
8
A
SER
451
69.78
111.08
8
A
GLU
452
-140.07
-71.43
9
A
SER
365
64.39
122.43
9
A
ASP
367
-50.53
-178.57
9
A
ARG
384
32.21
48.73
9
A
ALA
447
-85.65
33.80
9
A
ARG
450
-162.81
112.03
9
A
GLU
452
57.21
-89.80
10
A
ARG
384
33.39
47.62
10
A
ALA
447
-90.60
32.72
10
A
ILE
448
-163.19
116.13
10
A
ARG
450
-154.52
-85.98
10
A
SER
451
89.87
101.63
11
A
ARG
384
31.46
48.40
11
A
PRO
398
-78.39
46.84
11
A
ILE
448
32.83
60.34
11
A
ARG
450
-97.12
33.57
11
A
GLU
452
64.92
-84.49
12
A
LEU
366
60.60
154.74
12
A
ARG
384
20.37
50.91
12
A
PRO
398
-82.22
42.21
12
A
VAL
411
-60.18
98.90
12
A
ALA
447
-91.87
31.43
12
A
ILE
448
-161.43
93.19
12
A
ARG
450
81.98
53.92
12
A
GLU
452
78.62
-70.32
13
A
SER
365
-45.11
166.61
13
A
LEU
366
-123.31
-168.48
13
A
ASP
367
-62.78
-176.55
13
A
ARG
384
32.45
47.32
13
A
ILE
420
-49.57
-18.97
13
A
ALA
447
-94.49
32.10
14
A
LEU
366
65.19
147.68
14
A
LEU
383
-104.61
41.84
14
A
ARG
384
-43.53
85.39
14
A
PRO
398
-81.63
44.43
14
A
ALA
447
-87.57
33.29
14
A
ARG
450
163.64
78.20
14
A
GLU
452
162.13
-68.61
15
A
LEU
383
-88.80
40.88
15
A
ARG
384
-35.42
82.98
15
A
PRO
398
-76.66
48.04
15
A
THR
414
-163.94
114.30
15
A
ILE
448
-26.77
121.45
15
A
SER
451
-167.06
35.11
15
A
GLU
452
67.79
166.55
16
A
SER
365
54.24
-172.97
16
A
ARG
384
38.14
41.04
16
A
PRO
398
-78.04
47.37
16
A
ALA
446
-69.77
9.79
16
A
ILE
448
-36.13
98.15
16
A
ARG
450
-47.16
-71.50
16
A
SER
451
-66.62
-177.64
16
A
GLU
452
68.16
-69.95
17
A
SER
365
69.33
106.09
17
A
ASP
367
-110.28
-169.39
17
A
LEU
383
-88.05
40.99
17
A
ARG
384
-39.37
87.71
17
A
PRO
398
-78.76
49.12
17
A
ALA
447
-91.24
31.78
17
A
ARG
450
169.56
-57.87
17
A
SER
451
50.12
107.49
18
A
ARG
384
24.25
63.13
18
A
PRO
398
-81.31
43.93
18
A
ALA
446
-66.75
3.03
18
A
ILE
448
-34.95
104.68
18
A
GLU
452
64.76
-80.66
19
A
ARG
384
38.32
40.33
19
A
PRO
398
-74.43
46.10
19
A
THR
414
-161.52
115.79
19
A
ALA
447
-93.58
33.17
19
A
ILE
448
-9.90
123.52
19
A
PRO
449
-58.89
64.56
19
A
ARG
450
64.98
110.21
19
A
SER
451
174.15
41.56
19
A
GLU
452
66.29
-81.32
20
A
LEU
366
-109.36
-166.36
20
A
LEU
383
-89.42
41.41
20
A
ARG
384
-46.10
80.54
20
A
PRO
398
-77.58
45.07
20
A
VAL
411
-51.79
93.85
20
A
ALA
447
-88.00
31.37
20
A
ARG
450
-161.42
76.47
20
A
GLU
452
-178.47
-39.71
Solution structure of double-stranded RNA binding domain of S.cerevisiae RNase III (rnt1p)
1
N
N
A
ASN
369
A
ASN
6
HELX_P
A
ILE
378
A
ILE
15
1
1
10
A
ASN
419
A
ASN
56
HELX_P
A
ASP
434
A
ASP
71
1
2
16
A
ASP
434
A
ASP
71
HELX_P
A
ALA
447
A
ALA
84
1
3
14
RNA BINDING PROTEIN
DSRBD, RNT1P, RNA BINDING PROTEIN
RNT1_YEAST
UNP
1
366
Q02555
LDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQR
AAIPRSES
366
453
2LUQ
366
453
Q02555
A
1
3
90
1
expression tag
GLY
364
2LUQ
A
Q02555
UNP
1
1
expression tag
SER
365
2LUQ
A
Q02555
UNP
2
3
anti-parallel
anti-parallel
A
HIS
386
A
HIS
23
A
PRO
393
A
PRO
30
A
PRO
398
A
PRO
35
A
ARG
405
A
ARG
42
A
VAL
411
A
VAL
48
A
GLY
417
A
GLY
54