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Found 1 Document (0.827 seconds)

BMRB: 30008

5I1R

Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering

Authors

Deshmukh, L., Schwieters, C.D., Grishaev, A., Clore, G.M.

Assembly

Nucleocapsid protein p7

Entity

1. Nucleocapsid protein p7 (polymer, Thiol state: all other bound), 55 monomers, 6425.384 Da Detail

MQRGNFRNQR KIVKCFNCGK EGHTARNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

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

Total weight

6556.2017 Da

Max. entity weight

6425.384 Da

Entity Connection

na 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS15:SG	2:ZN1:ZN
2	na	sing	1:CYS18:SG	2:ZN1:ZN
3	na	sing	1:CYS28:SG	2:ZN1:ZN
4	na	sing	1:CYS36:SG	2:ZN1:ZN
5	na	sing	1:CYS39:SG	2:ZN1:ZN
6	na	sing	1:CYS49:SG	2:ZN1:ZN

Source organism

HIV-1 M:B_HXB2R

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.1 %, Completeness: 37.8 %, Completeness (bb): 70.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	37.8 % (249 of 659)	18.1 % (65 of 359)	58.5 % (138 of 236)	71.9 % (46 of 64)
Backbone	70.7 % (232 of 328)	44.3 % (51 of 115)	84.9 % (135 of 159)	85.2 % (46 of 54)
Sidechain	15.8 % (60 of 380)	5.7 % (14 of 244)	36.5 % (46 of 126)	0.0 % (0 of 10)
Aromatic	0.0 % (0 of 40)	0.0 % (0 of 20)	0.0 % (0 of 19)	0.0 % (0 of 1)
Methyl	16.7 % (3 of 18)	0.0 % (0 of 9)	33.3 % (3 of 9)

1. Nucleocapsid protein p7

MQRGNFRNQR KIVKCFNCGK EGHTARNCRA PRKKGCWKCG KEGHQMKDCT ERQAN

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Dithiothreitol	natural abundance	1 mM
2	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	zinc chloride	natural abundance	0.1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

Sample #2

#	Name	Isotope labeling	Concentration
8	Dithiothreitol	natural abundance	1 mM
9	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
10	neutral bicelles	natural abundance	5 %
11	sodium chloride	natural abundance	50 mM
12	sodium phosphate	natural abundance	20 mM
13	zinc chloride	natural abundance	0.1 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.2514495

Referencing offset: 0.5 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.2514495

Referencing offset: 0.5 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.2514495

Referencing offset: 0.59 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 5I1R, Strand ID: A Detail

Release date

2016-03-27

Citation

Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering
Deshmukh, L., Schwieters, C.D., Grishaev, A., Clore, G.M.
Chemphyschem. (2016), 17, 1548-1552, PubMed 26946052 , DOI 10.1002/cphc.201600212 , Abstract

Related entities 1. Nucleocapsid protein p7, : 1 : 2 : 2 : 4 : 156 entities Detail

Interaction partners 1. Nucleocapsid protein p7, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Dithiothreitol	natural abundance	1 mM
2	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	zinc chloride	natural abundance	0.1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

2 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Dithiothreitol	natural abundance	1 mM
2	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	zinc chloride	natural abundance	0.1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Dithiothreitol	natural abundance	1 mM
2	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	zinc chloride	natural abundance	0.1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Dithiothreitol	natural abundance	1 mM
2	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	zinc chloride	natural abundance	0.1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

5 2D ARTSY

Instrument

Bruker Avance - 800 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
8	Dithiothreitol	natural abundance	1 mM
9	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
10	neutral bicelles	natural abundance	5 %
11	sodium chloride	natural abundance	50 mM
12	sodium phosphate	natural abundance	20 mM
13	zinc chloride	natural abundance	0.1 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

6 3D Quntitaive HNCO - NC'

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
8	Dithiothreitol	natural abundance	1 mM
9	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
10	neutral bicelles	natural abundance	5 %
11	sodium chloride	natural abundance	50 mM
12	sodium phosphate	natural abundance	20 mM
13	zinc chloride	natural abundance	0.1 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

7 3D Quntitaive HNCO - CaC'

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
8	Dithiothreitol	natural abundance	1 mM
9	Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1)	[U-13C; U-15N; U-2H]	0.2 mM
10	neutral bicelles	natural abundance	5 %
11	sodium chloride	natural abundance	50 mM
12	sodium phosphate	natural abundance	20 mM
13	zinc chloride	natural abundance	0.1 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_30008_5i1r.nef
Input source #2: Coordindates	5i1r.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)
1:15:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:18:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:23:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:28:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:36:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:44:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:49:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

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

Sequence alignments

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

--380-----390-------400-------410-------420-------430--
MQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN
--------10--------20--------30--------40--------50-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	55	0	0	100.0

Content subtype: combined_30008_5i1r.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	209		83.6 (chain: A, length: 55)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 83.6%
- Total number of assignments
  - ¹³C chemical shifts: 125
  - ¹H chemical shifts: 42
  - ¹⁵N chemical shifts: 42
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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 (%)
¹³C chemical shifts	236	125	53.0
¹H chemical shifts	359	42	11.7
¹⁵N chemical shifts	71	42	59.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	110	85	77.3
¹H chemical shifts	115	42	36.5
¹⁵N chemical shifts	54	42	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	126	40	31.7
¹H chemical shifts	244	0	0.0
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	11	3	27.3
¹H chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	19	0	0.0
¹H chemical shifts	20	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords VIRAL PROTEIN

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Found 1 Document (0.827 seconds)

BMRB: 30008

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Nucleocapsid protein p7, : 1 : 2 : 2 : 4 : 156 entities Detail

Interaction partners 1. Nucleocapsid protein p7, : 5 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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NMR combined restraints 2 contents Detail