BMRB Entry 15113

Name: Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:muPsi RNA Packaging Signal Complex
Published: 2007-03-05

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PDB ID: 2ihx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15113
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2007-01-24

Original release date:

2007-03-05

Authors:

Zhou, J.; Summers, M.

Citation:

Citation: Zhou, J.; Bean, R.; Vogt, V.; Summers, M.. "Solution Structure of the Rous Sarcoma Virus Nucleocaspid Protein:muPsi RNA Packaging Signal Complex" J. Mol. Biol. 365, 453-467 (2007).
PubMed: 17070546

Assembly members:

Assembly members:
ZN, non-polymer, Formula weight is not available
muPsi_RNA, polymer, 75 residues, Formula weight is not available
Nucleocapsid_(NC)_Protein, polymer, 61 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: 11886 Superkingdom: Viruses Kingdom: not available Genus/species: Alpharetrovirus Rous sarcoma virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6P-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
muPsi_RNA: CUGCCCUCAUCCGUCUCGCU UAUUCGGGGAGCGGACGAUG ACCCUAGUAGAGGGGGCUGC GGCUUAGGAGGGCAG
Nucleocapsid_(NC)_Protein: GRARGLCYTCGSPGHYQAQC PKKRKSGNSRERCQLCNGMG HNAKQCRKRDGNQGQRPGKG L

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	88
1H chemical shifts	567

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Zn	1
2	muPsi RNA	2
3	NC protein	3

Entities:

Entity 1, Zn - Formula weight is not available

1

ZN

Entity 2, muPsi RNA 75 residues - Formula weight is not available

1

C

U

G

C

U

C

A

U

2

C

G

U

C

U

C

G

C

U

3

U

A

U

C

G

A

4

G

C

G

A

C

G

A

U

G

5

A

C

U

A

G

U

A

G

6

A

G

C

U

G

C

7

G

C

U

A

G

A

G

8

G

C

A

G

Entity 3, NC protein 61 residues - Formula weight is not available

1

GLY

ARG

ALA

ARG

GLY

LEU

CYS

TYR

THR

CYS

2

GLY

SER

PRO

GLY

HIS

TYR

GLN

ALA

GLN

CYS

3

PRO

LYS

ARG

LYS

SER

GLY

ASN

SER

ARG

4

GLU

ARG

CYS

GLN

LEU

CYS

ASN

GLY

MET

GLY

5

HIS

ASN

ALA

LYS

GLN

CYS

ARG

LYS

ARG

ASP

6

GLY

ASN

GLN

GLY

GLN

ARG

PRO

GLY

LYS

GLY

7

LEU

Samples:

sample_1: muPsi RNA, G, C, U 2H-enriched, 1.0 mM; Nucleocapsid (NC) Protein 1.0 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_2: muPsi RNA, A, C, U 2H-enriched, 1.2 mM; Nucleocapsid (NC) Protein 1.2 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_3: muPsi RNA, A, G, C 2H-enriched, 0.8 mM; Nucleocapsid (NC) Protein 0.8 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_4: muPsi RNA, A, G, U 2H-enriched, 0.8 mM; Nucleocapsid (NC) Protein 0.8 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_5: muPsi RNA 1.2 mM; Nucleocapsid (NC) Protein 1.2 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_6: muPsi RNA 1.2 mM; Nucleocapsid (NC) Protein, [U-98% 13C; U-98% 15N], 1.2 mM; Tris-d11-HCl 5 mM; NaCL 5 mM; ZnCl2 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 0.0053 M; pH: 7.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_3	isotropic	sample_conditions_1
2D NOESY	sample_4	isotropic	sample_conditions_1
2D NOESY	sample_5	isotropic	sample_conditions_1
3D_13C-separated_NOESY	sample_6	isotropic	sample_conditions_1

Software:

xwinnmr, BRUKER - collection

NMRPipe, Delaglio, F., Grzesiek. S., Vuister, G.W., Zhu, G., Pfeifer, J., & Bax, A. - processing

NMRView v5, Johnson, B.A., Blevins, R.A. - data analysis

CYANA v2.1, Guntert, P., Mumenthaler, C. & Wuthrich, K. - refinement

NMR spectrometers:

Bruker DRX 800 MHz
Bruker DMX 600 MHz

PDB	2IHX 5A9E
EMBL	CAA24512
GB	AAB59932 AAB59933 AAC82560 AAC82561 ABD83647
REF	NP_056886 NP_056887 NP_955610
SP	P03322 P03354
AlphaFold	P03322 P03354