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Found 1 Document (0.647 seconds)

BMRB: 15113

2IHX

Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:muPsi RNA Packaging Signal Complex

Authors

Zhou, J., Summers, M.F.

Assembly

NC:muPsi complex

Entity

1. ZN (non-polymer), 65.409 Da
2. muPsi RNA (polymer, Thiol state: not present), 75 monomers, 24330.36 Da Detail

CUGCCCUCAU CCGUCUCGCU UAUUCGGGGA GCGGACGAUG ACCCUAGUAG AGGGGGCUGC GGCUUAGGAG GGCAG

3. Nucleocapsid (NC) Protein (polymer, Thiol state: all other bound), 61 monomers, 6690.550 Da Detail

GRARGLCYTC GSPGHYQAQC PKKRKSGNSR ERCQLCNGMG HNAKQCRKRD GNQGQRPGKG L

Total weight

31086.316 Da

Max. entity weight

24330.36 Da

Source organism

Rous sarcoma virus

Exptl. method

solution NMR

Refine. method

1H-1H distance restraints, Hydrogen-bond restraints, Torsion angle restraints, Inter-phosphate restraints

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.6 %, Completeness: 36.9 %, Completeness (bb): 34.4 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C
All	36.9 % (653 of 1768)	54.5 % (560 of 1028)	12.6 % (93 of 740)
Backbone	34.4 % (388 of 1127)	56.9 % (330 of 580)	10.6 % (58 of 547)
Sidechain	42.1 % (291 of 691)	51.3 % (230 of 448)	25.1 % (61 of 243)
Aromatic	44.1 % (137 of 311)	73.4 % (130 of 177)	5.2 % (7 of 134)
Methyl	80.0 % (16 of 20)	80.0 % (8 of 10)	80.0 % (8 of 10)

2. muPsi RNA

CUGCCCUCAU CCGUCUCGCU UAUUCGGGGA GCGGACGAUG ACCCUAGUAG AGGGGGCUGC GGCUUAGGAG GGCAG

3. Nucleocapsid (NC) Protein

GRARGLCYTC GSPGHYQAQC PKKRKSGNSR ERCQLCNGMG HNAKQCRKRD GNQGQRPGKG L

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.0 mM unlabeled nucleocapsid protein, 1.0 mM A-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
1	muPsi RNA	G, C, U 2H-enriched	1.0 mM
2	Nucleocapsid (NC) Protein	natural abundance	1.0 mM
3	Tris-d11-HCl		5 mM
4	NaCL		5 mM
5	ZnCl2		0.1 mM
6	D2O		100 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM unlabeled nucleocapsid protein, 1.2 mM G-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
7	muPsi RNA	A, C, U 2H-enriched	1.2 mM
8	Nucleocapsid (NC) Protein	natural abundance	1.2 mM
9	Tris-d11-HCl		5 mM
10	NaCL		5 mM
11	ZnCl2		0.1 mM
12	D2O		100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 0.8 mM unlabeled nucleocapsid protein, 0.8 mM U-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
13	muPsi RNA	A, G, C 2H-enriched	0.8 mM
14	Nucleocapsid (NC) Protein	natural abundance	0.8 mM
15	Tris-d11-HCl		5 mM
16	NaCL		5 mM
17	ZnCl2		0.1 mM
18	D2O		100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 0.8 mM unlabeled nucleocapsid protein, 0.8 mM C-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
19	muPsi RNA	A, G, U 2H-enriched	0.8 mM
20	Nucleocapsid (NC) Protein	natural abundance	0.8 mM
21	Tris-d11-HCl		5 mM
22	NaCL		5 mM
23	ZnCl2		0.1 mM
24	D2O		100 %

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM unlabeled nucleocapsid protein, 1.2 mM unlabeled muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
25	muPsi RNA	natural abundance	1.2 mM
26	Nucleocapsid (NC) Protein	natural abundance	1.2 mM
27	Tris-d11-HCl		5 mM
28	NaCL		5 mM
29	ZnCl2		0.1 mM
30	D2O		100 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM 15N, 13C-labeled nucleocapsid protein, 1.2 mM unlabeled muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0; 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
31	muPsi RNA	natural abundance	1.2 mM
32	Nucleocapsid (NC) Protein	[U-98% 13C; U-98% 15N]	1.2 mM
33	Tris-d11-HCl		5 mM
34	NaCL		5 mM
35	ZnCl2		0.1 mM
36	D2O		100 %

Protein Blocks Logo

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

Release date

2007-03-04

Citation

Solution structure of the Rous sarcoma virus nucleocapsid protein: muPsi RNA packaging signal complex
Zhou, J., Bean, R.L., Vogt, V.M., Summers, M.F.
J. Mol. Biol. (2007), 365, 453-467, PubMed 17070546 , DOI 10.1016/j.jmb.2006.10.013 , Abstract

Related entities 2. muPsi RNA, : 1 entities Detail

Related entities 3. Nucleocapsid (NC) Protein, : 1 : 3 : 2 : 45 entities Detail

Experiments performed 6 experiments Detail

1 2D NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.0 mM unlabeled nucleocapsid protein, 1.0 mM A-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
1	muPsi RNA	G, C, U 2H-enriched	1.0 mM
2	Nucleocapsid (NC) Protein	natural abundance	1.0 mM
3	Tris-d11-HCl		5 mM
4	NaCL		5 mM
5	ZnCl2		0.1 mM
6	D2O		100 %

2 2D NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM unlabeled nucleocapsid protein, 1.2 mM G-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
7	muPsi RNA	A, C, U 2H-enriched	1.2 mM
8	Nucleocapsid (NC) Protein	natural abundance	1.2 mM
9	Tris-d11-HCl		5 mM
10	NaCL		5 mM
11	ZnCl2		0.1 mM
12	D2O		100 %

3 2D NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 0.8 mM unlabeled nucleocapsid protein, 0.8 mM U-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
13	muPsi RNA	A, G, C 2H-enriched	0.8 mM
14	Nucleocapsid (NC) Protein	natural abundance	0.8 mM
15	Tris-d11-HCl		5 mM
16	NaCL		5 mM
17	ZnCl2		0.1 mM
18	D2O		100 %

4 2D NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 0.8 mM unlabeled nucleocapsid protein, 0.8 mM C-selectively-protonated muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
19	muPsi RNA	A, G, U 2H-enriched	0.8 mM
20	Nucleocapsid (NC) Protein	natural abundance	0.8 mM
21	Tris-d11-HCl		5 mM
22	NaCL		5 mM
23	ZnCl2		0.1 mM
24	D2O		100 %

5 2D NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM unlabeled nucleocapsid protein, 1.2 mM unlabeled muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
25	muPsi RNA	natural abundance	1.2 mM
26	Nucleocapsid (NC) Protein	natural abundance	1.2 mM
27	Tris-d11-HCl		5 mM
28	NaCL		5 mM
29	ZnCl2		0.1 mM
30	D2O		100 %

6 3D_13C-separated_NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7.0, Details 1.2 mM 15N, 13C-labeled nucleocapsid protein, 1.2 mM unlabeled muPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0; 5mM NaCl, 0.1 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
31	muPsi RNA	natural abundance	1.2 mM
32	Nucleocapsid (NC) Protein	[U-98% 13C; U-98% 15N]	1.2 mM
33	Tris-d11-HCl		5 mM
34	NaCL		5 mM
35	ZnCl2		0.1 mM
36	D2O		100 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_15113_2ihx.nef
Input source #2: Coordindates	2ihx.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
3:1:ZN:ZN	2:7:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	2:10:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	2:20:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	2:15:HIS:NE2	unknown	unknown	n/a
3:2:ZN:ZN	2:41:HIS:NE2	unknown	unknown	n/a
3:2:ZN:ZN	2:46:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	2:33:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	2:36:CYS:SG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	None
C	2	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A
Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	75	0	0	100.0
A	A	61	0	0	100.0

Content subtype: combined_15113_2ihx.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	639		54.1 (chain: A, length: 61), 100.0 (chain: B, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 54.1%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 551
  - ¹³C chemical shifts: 88
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	373	141	37.8
¹³C chemical shifts	243	88	36.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	35	26.9
¹³C chemical shifts	122	28	23.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	243	106	43.6
¹³C chemical shifts	121	60	49.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	8	72.7
¹³C chemical shifts	11	8	72.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	8	66.7
¹³C chemical shifts	12	7	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	655	410	62.6
¹³C chemical shifts	497	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	450	288	64.0
¹³C chemical shifts	375	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	205	122	59.5
¹³C chemical shifts	122	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	52	100.0
¹³C chemical shifts	52	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords nucleocapsid (NC) protein, psi-site, ribonucleic acid (RNA), Rous sarcoma virus, UNCG tetraloop, Protein-RNA complex

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Found 1 Document (0.647 seconds)

BMRB: 15113

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Related entities 2. muPsi RNA, : 1 entities Detail

Related entities 3. Nucleocapsid (NC) Protein, : 1 : 3 : 2 : 45 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 2 contents Detail