BMRB: 25100

Solution NMR structure pf tRNApro:MLV-Nucleocapsid (1:2) Complex

Authors

D'Souza, V., Yildiz, Z.

Assembly

pf tRNApro:MLV-Nucleocapsid (1:2) Complex

Entity

1. MLV Nucleocapsid (polymer), 55 monomers, 6248.968 Da Detail

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER) (polymer, Thiol state: not present), 74 monomers, 23947.10 × 2 Da Detail

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

3. ZINC ION (non-polymer), 65.409 × 2 Da

Total weight

54273.984 Da

Max. entity weight

23947.1 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: 17.1 %, Completeness: 4.0 %, Completeness (bb): 2.9 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	4.0 % (69 of 1723)	5.5 % (55 of 997)	1.9 % (14 of 726)
Backbone	2.9 % (31 of 1084)	3.8 % (21 of 555)	1.9 % (10 of 529)
Sidechain	6.1 % (42 of 688)	7.7 % (34 of 442)	3.3 % (8 of 246)
Aromatic	0.0 % (0 of 310)	0.0 % (0 of 177)	0.0 % (0 of 133)
Methyl	7.7 % (2 of 26)	15.4 % (2 of 13)	0.0 % (0 of 13)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete2

Sequence coverage: 24.0 %, Completeness: 4.5 %, Completeness (bb): 3.0 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	4.5 % (154 of 3446)	6.7 % (134 of 1994)	1.4 % (20 of 1452)
Backbone	3.0 % (66 of 2168)	4.7 % (52 of 1110)	1.3 % (14 of 1058)
Sidechain	6.8 % (93 of 1376)	9.3 % (82 of 884)	2.2 % (11 of 492)
Aromatic	1.5 % (9 of 620)	2.5 % (9 of 354)	0.0 % (0 of 266)
Methyl	11.5 % (6 of 52)	15.4 % (4 of 26)	7.7 % (2 of 26)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete3

Sequence coverage: 46.5 %, Completeness: 5.8 %, Completeness (bb): 3.7 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	5.8 % (300 of 5169)	9.4 % (280 of 2991)	0.9 % (20 of 2178)
Backbone	3.7 % (120 of 3252)	6.4 % (106 of 1665)	0.9 % (14 of 1587)
Sidechain	9.0 % (186 of 2064)	13.2 % (175 of 1326)	1.5 % (11 of 738)
Aromatic	11.0 % (102 of 930)	19.2 % (102 of 531)	0.0 % (0 of 399)
Methyl	7.7 % (6 of 78)	10.3 % (4 of 39)	5.1 % (2 of 39)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete4

Sequence coverage: 3.9 %, Completeness: 4.8 %, Completeness (bb): 3.3 % Detail

Download

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	4.8 % (330 of 6892)	7.8 % (310 of 3988)	0.7 % (20 of 2904)
Backbone	3.3 % (144 of 4336)	5.9 % (130 of 2220)	0.7 % (14 of 2116)
Sidechain	7.0 % (192 of 2752)	10.2 % (181 of 1768)	1.1 % (11 of 984)
Aromatic	8.7 % (108 of 1240)	15.3 % (108 of 708)	0.0 % (0 of 532)
Methyl	5.8 % (6 of 104)	7.7 % (4 of 52)	3.8 % (2 of 52)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete5

Sequence coverage: 26.4 %, Completeness: 4.3 %, Completeness (bb): 3.0 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	4.3 % (368 of 8615)	6.3 % (315 of 4985)	1.5 % (53 of 3630)
Backbone	3.0 % (160 of 5420)	4.8 % (132 of 2775)	1.1 % (28 of 2645)
Sidechain	6.2 % (214 of 3440)	8.3 % (184 of 2210)	2.4 % (30 of 1230)
Aromatic	8.2 % (127 of 1550)	12.2 % (108 of 885)	2.9 % (19 of 665)
Methyl	6.2 % (8 of 130)	9.2 % (6 of 65)	3.1 % (2 of 65)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Chem. Shift Complete6

Sequence coverage: 5.4 %, Completeness: 4.0 %, Completeness (bb): 2.9 % Detail

Download

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C
All	4.0 % (409 of 10338)	5.9 % (350 of 5982)	1.4 % (59 of 4356)
Backbone	2.9 % (187 of 6504)	4.6 % (153 of 3330)	1.1 % (34 of 3174)
Sidechain	5.6 % (230 of 4128)	7.5 % (198 of 2652)	2.2 % (32 of 1476)
Aromatic	7.1 % (132 of 1860)	10.6 % (113 of 1062)	2.4 % (19 of 798)
Methyl	6.4 % (10 of 156)	10.3 % (8 of 78)	2.6 % (2 of 78)

1. MLV Nucleocapsid

ATVVSGQKQD RQGGERRRSQ LDRDQCAYCK EKGHWAKDCP KKPRGPRGPR PQTSL

2. RNA (71-MER)

GGCUCGUUGG UCUAGGGGUA UGAUUCUCGC UUAGGGUGCG AGAGGUCCCG GGUUCAAAUC CCGGACGAGC CCCA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	NC-tRNApro (1:1)	natural abundance		0.5 mM
2	MgCl2	natural abundance		1 mM
3	NaCl	natural abundance		10 mM
4	Tris	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
8	MgCl2	natural abundance		1 mM
9	NaCl	natural abundance		10 mM
10	Tris	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	NC-tRNApro (1:1)	13C, 15N G-lab tRNA-pro		0.5 mM
14	MgCl2	natural abundance		1 mM
15	NaCl	natural abundance		10 mM
16	Tris	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Hide sample codition

Protein Blocks Logo

Calculated from 10 models in PDB: 2MS0, Strand ID: A, C Detail

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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 , Abstract

Related entities 1. MLV Nucleocapsid, : 1 : 9 : 1 : 23 entities Detail

Related entities 2. RNA (71-MER), : 1 : 9 entities Detail

Interaction partners 1. MLV Nucleocapsid, : 1 interactors Detail

Experiments performed 7 experiments Detail