BMRBj - BMREntryMaster

Found 1 Document (0.799 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.799 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 2 contents Detail