BMRB: 19609

Solution Structure of Protein-RNA Ternary Complex

Authors

Takahashi, M., Kuwasako, K., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Guntert, P., Shirouzu, M., Ito, T., Tanaka, A., Yokoyama, S., Hagiwara, M., Kuroyanagi, H., Muto, Y.

Assembly

Protein-RNA Ternary Complex

Entity

1. Protein-RNA Ternary Complex, entity 1 (polymer, Thiol state: unknown), 94 monomers, 10570.88 Da Detail

GDGPRRLHVS NIPFKYREPD LTAMFEKVGP VVDVEIIFNE RGSKGFGFVT MQNPDDADRA RAEFNGTTIE GRRVEVNLAT QRVHNKKAKP LMSV

2. Protein-RNA Ternary Complex, entity 2 (polymer, Thiol state: unknown), 105 monomers, 11594.88 Da Detail

GSTNAEPVVG SRDTMFTKIF VGGLPYHTSD KTLHEYFEQF GDIEEAVVIT DRNTQKSRGY GFVTMKDRAS AERACKDPNP IIDGRKANVN LAYLGAKPRT NVQLA

3. RNA (polymer, Thiol state: not present), 12 monomers, 3908.276 Da Detail

UGCAUGGUGU GC

Total weight

26074.035 Da

Max. entity weight

11594.88 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 50.2 %, Completeness: 41.5 %, Completeness (bb): 39.8 % Detail

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• NMR-STAR v3.1 (partial)
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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	41.5 % (1030 of 2480)	43.7 % (568 of 1299)	36.8 % (356 of 967)	49.5 % (106 of 214)
Backbone	39.8 % (519 of 1304)	43.1 % (205 of 476)	33.8 % (216 of 640)	52.1 % (98 of 188)
Sidechain	44.5 % (604 of 1358)	44.1 % (363 of 823)	45.6 % (232 of 509)	34.6 % (9 of 26)
Aromatic	32.4 % (72 of 222)	33.3 % (37 of 111)	34.3 % (35 of 102)	0.0 % (0 of 9)
Methyl	54.5 % (110 of 202)	55.4 % (56 of 101)	53.5 % (54 of 101)

1. entity 1

GDGPRRLHVS NIPFKYREPD LTAMFEKVGP VVDVEIIFNE RGSKGFGFVT MQNPDDADRA RAEFNGTTIE GRRVEVNLAT QRVHNKKAKP LMSV

2. entity 2

GSTNAEPVVG SRDTMFTKIF VGGLPYHTSD KTLHEYFEQF GDIEEAVVIT DRNTQKSRGY GFVTMKDRAS AERACKDPNP IIDGRKANVN LAYLGAKPRT NVQLA

3. RNA

UGCAUGGUGU GC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6 (±1), Details 20mMd-Tris-HCl(pH7.0),100mMNaCl,1mMd-DTT,0.02%NaN3

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	protein	0.7 mM
2	entity_2	[U-99% 13C; U-99% 15N]	protein	0.7 mM
3	RNA	natural abundance	RNA	0.7 mM
4	H2O		solvent	90 %
5	D2O		solvent	10 %
6	d-Tris-HCl		buffer	20 mM
7	NaCl	natural abundance	salt	100 mM
8	d-DTT			1 mM
9	NaN3	natural abundance		0.02 %

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Chem. Shift Complete2

Sequence coverage: 50.7 %, Completeness: 42.1 %, Completeness (bb): 39.5 % Detail

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• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	42.1 % (2086 of 4960)	45.3 % (1178 of 2598)	36.3 % (702 of 1934)	48.1 % (206 of 428)
Backbone	39.5 % (1030 of 2608)	44.2 % (421 of 952)	32.6 % (417 of 1280)	51.1 % (192 of 376)
Sidechain	45.6 % (1238 of 2716)	46.0 % (757 of 1646)	45.8 % (466 of 1018)	28.8 % (15 of 52)
Aromatic	37.8 % (168 of 444)	39.6 % (88 of 222)	39.2 % (80 of 204)	0.0 % (0 of 18)
Methyl	52.0 % (210 of 404)	53.0 % (107 of 202)	51.0 % (103 of 202)

1. entity 1

GDGPRRLHVS NIPFKYREPD LTAMFEKVGP VVDVEIIFNE RGSKGFGFVT MQNPDDADRA RAEFNGTTIE GRRVEVNLAT QRVHNKKAKP LMSV

2. entity 2

GSTNAEPVVG SRDTMFTKIF VGGLPYHTSD KTLHEYFEQF GDIEEAVVIT DRNTQKSRGY GFVTMKDRAS AERACKDPNP IIDGRKANVN LAYLGAKPRT NVQLA

3. RNA

UGCAUGGUGU GC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6 (±1), Details 20mMd-Tris-HCl(pH7.0),100mMNaCl,1mMd-DTT,0.02%NaN3

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	protein	0.7 mM
2	entity_2	[U-99% 13C; U-99% 15N]	protein	0.7 mM
3	RNA	natural abundance	RNA	0.7 mM
4	H2O		solvent	90 %
5	D2O		solvent	10 %
6	d-Tris-HCl		buffer	20 mM
7	NaCl	natural abundance	salt	100 mM
8	d-DTT			1 mM
9	NaN3	natural abundance		0.02 %

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LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 2MGZ, Strand ID: A, B Detail

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Release date

2014-08-10

Citation

Solution Structure of Protein-RNA Ternary Complex
Kuwasako, K., Takahashi, M., Unzai, S., Tsuda, K., Yoshikawa, S., He, F., Kobayashi, N., Guntert, P., Shirouzu, M., Ito, T., Tanaka, A., Yokoyama, S., Hagiwara, M., Kuroyanagi, H., Muto, Y.
Not known

Related entities 1. Protein-RNA Ternary Complex, entity 1, : 1 : 1 : 305 entities Detail

Related entities 2. Protein-RNA Ternary Complex, entity 2, : 1 : 2 : 100 entities Detail

Related entities 3. RNA, : 1 entities Detail

Experiments performed 6 experiments Detail