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Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) Complex
Authors
D'Souza, V., Yildiz, Z.
Assembly
tRNApro:MLV Nucleocapsid Protein (1:1) Complex
Entity
1. MLV Nucleocapsid (polymer), 55 monomers, 6248.968 Da Detail

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL


2. tRNApro (polymer, Thiol state: not present), 71 monomers, 23007.53 Da Detail

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC C


3. ZINC ION (non-polymer), 65.409 Da
Total weight
29321.904 Da
Max. entity weight
23007.53 Da
Source organism
Murine leukemia virus , Homo sapiens
Exptl. method
solution NMR
Refine. method
distance geometry
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 31.0 %, Completeness: 5.9 %, Completeness (bb): 3.6 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C
All 5.9 % (99 of 1674)10.0 % (97 of 969) 0.3 % (2 of 705)
Backbone 3.6 % (38 of 1051) 6.7 % (36 of 537) 0.4 % (2 of 514)
Sidechain 9.1 % (61 of 672)14.1 % (61 of 432) 0.0 % (0 of 240)
Aromatic 8.1 % (24 of 298)14.0 % (24 of 171) 0.0 % (0 of 127)
Methyl 0.0 % (0 of 26) 0.0 % (0 of 13) 0.0 % (0 of 13)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. tRNApro

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC C

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
1NC-tRNApro (1:1)natural abundance0.5 mM
2MgCl2natural abundance1 mM
3NaClnatural abundance10 mM
4Trisnatural abundance10 mM
5H2Onatural abundance90 %
6D2Onatural abundance10 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
7NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
8MgCl2natural abundance1 mM
9NaClnatural abundance10 mM
10Trisnatural abundance10 mM
11H2Onatural abundance90 %
12D2Onatural abundance10 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
13NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro13C0.5 mM
14MgCl2natural abundance1 mM
15NaClnatural abundance10 mM
16Trisnatural abundance10 mM
17H2Onatural abundance90 %
18D2Onatural abundance10 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
19NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
20MgCl2natural abundance1 mM
21NaClnatural abundance10 mM
22Trisnatural abundance10 mM
23H2Onatural abundance90 %
24D2Onatural abundance10 %
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
25NC-tRNApro (1:1)13C, 15N G-lab tRNA-13C0.5 mM
26MgCl2natural abundance1 mM
27NaClnatural abundance10 mM
28Trisnatural abundance10 mM
29H2Onatural abundance90 %
30D2Onatural abundance10 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
31NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
32MgCl2natural abundance1 mM
33NaClnatural abundance10 mM
34Trisnatural abundance10 mM
35H2Onatural abundance90 %
36D2Onatural abundance10 %

Chem. Shift Complete2
Sequence coverage: 43.7 %, Completeness: 7.0 %, Completeness (bb): 4.5 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C
All 7.0 % (236 of 3348)11.9 % (230 of 1938) 0.4 % (6 of 1410)
Backbone 4.5 % (94 of 2102) 8.2 % (88 of 1074) 0.6 % (6 of 1028)
Sidechain10.7 % (144 of 1344)16.6 % (143 of 864) 0.2 % (1 of 480)
Aromatic17.3 % (103 of 596)30.1 % (103 of 342) 0.0 % (0 of 254)
Methyl 0.0 % (0 of 52) 0.0 % (0 of 26) 0.0 % (0 of 26)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. tRNApro

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC C

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
1NC-tRNApro (1:1)natural abundance0.5 mM
2MgCl2natural abundance1 mM
3NaClnatural abundance10 mM
4Trisnatural abundance10 mM
5H2Onatural abundance90 %
6D2Onatural abundance10 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
7NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
8MgCl2natural abundance1 mM
9NaClnatural abundance10 mM
10Trisnatural abundance10 mM
11H2Onatural abundance90 %
12D2Onatural abundance10 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
13NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro13C0.5 mM
14MgCl2natural abundance1 mM
15NaClnatural abundance10 mM
16Trisnatural abundance10 mM
17H2Onatural abundance90 %
18D2Onatural abundance10 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
19NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
20MgCl2natural abundance1 mM
21NaClnatural abundance10 mM
22Trisnatural abundance10 mM
23H2Onatural abundance90 %
24D2Onatural abundance10 %
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
25NC-tRNApro (1:1)13C, 15N G-lab tRNA-13C0.5 mM
26MgCl2natural abundance1 mM
27NaClnatural abundance10 mM
28Trisnatural abundance10 mM
29H2Onatural abundance90 %
30D2Onatural abundance10 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
31NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
32MgCl2natural abundance1 mM
33NaClnatural abundance10 mM
34Trisnatural abundance10 mM
35H2Onatural abundance90 %
36D2Onatural abundance10 %

Chem. Shift Complete3
Sequence coverage: 27.8 %, Completeness: 5.7 %, Completeness (bb): 3.7 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C
All 5.7 % (284 of 5022) 8.2 % (237 of 2907) 2.2 % (47 of 2115)
Backbone 3.7 % (117 of 3153) 5.6 % (91 of 1611) 1.7 % (26 of 1542)
Sidechain 8.5 % (171 of 2016)11.3 % (147 of 1296) 3.3 % (24 of 720)
Aromatic13.6 % (122 of 894)20.1 % (103 of 513) 5.0 % (19 of 381)
Methyl 0.0 % (0 of 78) 0.0 % (0 of 39) 0.0 % (0 of 39)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. tRNApro

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC C

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
1NC-tRNApro (1:1)natural abundance0.5 mM
2MgCl2natural abundance1 mM
3NaClnatural abundance10 mM
4Trisnatural abundance10 mM
5H2Onatural abundance90 %
6D2Onatural abundance10 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
7NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
8MgCl2natural abundance1 mM
9NaClnatural abundance10 mM
10Trisnatural abundance10 mM
11H2Onatural abundance90 %
12D2Onatural abundance10 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
13NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro13C0.5 mM
14MgCl2natural abundance1 mM
15NaClnatural abundance10 mM
16Trisnatural abundance10 mM
17H2Onatural abundance90 %
18D2Onatural abundance10 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
19NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
20MgCl2natural abundance1 mM
21NaClnatural abundance10 mM
22Trisnatural abundance10 mM
23H2Onatural abundance90 %
24D2Onatural abundance10 %
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
25NC-tRNApro (1:1)13C, 15N G-lab tRNA-13C0.5 mM
26MgCl2natural abundance1 mM
27NaClnatural abundance10 mM
28Trisnatural abundance10 mM
29H2Onatural abundance90 %
30D2Onatural abundance10 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
31NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
32MgCl2natural abundance1 mM
33NaClnatural abundance10 mM
34Trisnatural abundance10 mM
35H2Onatural abundance90 %
36D2Onatural abundance10 %

Chem. Shift Complete4
Sequence coverage: 4.8 %, Completeness: 4.8 %, Completeness (bb): 3.5 % Detail

Polymer type: polypeptide(L) polyribonucleotide

Total1H13C
All 4.8 % (319 of 6696) 6.9 % (267 of 3876) 1.8 % (52 of 2820)
Backbone 3.5 % (146 of 4204) 5.4 % (115 of 2148) 1.5 % (31 of 2056)
Sidechain 6.7 % (179 of 2688) 8.9 % (153 of 1728) 2.7 % (26 of 960)
Aromatic10.7 % (128 of 1192)15.9 % (109 of 684) 3.7 % (19 of 508)
Methyl 0.0 % (0 of 104) 0.0 % (0 of 52) 0.0 % (0 of 52)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. tRNApro

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC C

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
1NC-tRNApro (1:1)natural abundance0.5 mM
2MgCl2natural abundance1 mM
3NaClnatural abundance10 mM
4Trisnatural abundance10 mM
5H2Onatural abundance90 %
6D2Onatural abundance10 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
7NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
8MgCl2natural abundance1 mM
9NaClnatural abundance10 mM
10Trisnatural abundance10 mM
11H2Onatural abundance90 %
12D2Onatural abundance10 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
13NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro13C0.5 mM
14MgCl2natural abundance1 mM
15NaClnatural abundance10 mM
16Trisnatural abundance10 mM
17H2Onatural abundance90 %
18D2Onatural abundance10 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
19NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
20MgCl2natural abundance1 mM
21NaClnatural abundance10 mM
22Trisnatural abundance10 mM
23H2Onatural abundance90 %
24D2Onatural abundance10 %
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
25NC-tRNApro (1:1)13C, 15N G-lab tRNA-13C0.5 mM
26MgCl2natural abundance1 mM
27NaClnatural abundance10 mM
28Trisnatural abundance10 mM
29H2Onatural abundance90 %
30D2Onatural abundance10 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 311 K, pH 7.2


#NameIsotope labelingTypeConcentration
31NC-tRNApro (1:1)13C, 15N G-lab tRNA-pro0.5 mM
32MgCl2natural abundance1 mM
33NaClnatural abundance10 mM
34Trisnatural abundance10 mM
35H2Onatural abundance90 %
36D2Onatural abundance10 %

Protein Blocks Logo
Calculated from 10 models in PDB: 2MS1, Strand ID: A Detail


Release date
2015-10-15
Citation
A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing
Miller, S.B., Yildiz, F.ZEHRA., Lo, J.A., Wang, B., D'Souza, V.M.
Nature (2014), 515, 591-595, PubMed 25209668 , DOI 10.1038/nature13709 ,
Related entities 1. MLV Nucleocapsid, : 1 : 9 : 1 : 23 entities Detail
Related entities 2. tRNApro, : 1 : 7 : 2 entities Detail
Interaction partners 1. MLV Nucleocapsid, : 1 interactors Detail
Experiments performed 10 experiments Detail
nullKeywords RNA/PROTEIN