BMRBj - BMREntryMaster

Found 1 Document (0.952 seconds)

BMRB: 5973

1R6R

Solution Structure of Dengue Virus Capsid Protein Reveals a New Fold

Authors

Ma, L., Jones, C.T., Groesch, T.D., Kuhn, R.J., Post, C.B.

Assembly

Dengue type 2 virus capsid protein

Entity

1. Dengue type 2 virus capsid protein (polymer, Thiol state: not present), 100 monomers, 11766.07 × 2 Da Detail

MNDQRKKARN TPFNMLKRER NRVSTVQQLT KRFSLGMLQG RGPLKLFMAL VAFLRFLTIP PTAGILKRWG TIKKSKAINV LRGFRKEIGR MLNILNRRRR

Total weight

23532.14 Da

Max. entity weight

11766.07 Da

Source organism

Dengue virus

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.0 %, Completeness: 78.7 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.7 % (1007 of 1279)	74.8 % (513 of 686)	81.0 % (393 of 485)	93.5 % (101 of 108)
Backbone	90.5 % (536 of 592)	94.6 % (192 of 203)	86.3 % (253 of 293)	94.8 % (91 of 96)
Sidechain	71.4 % (557 of 780)	66.5 % (321 of 483)	79.3 % (226 of 285)	83.3 % (10 of 12)
Aromatic	69.4 % (50 of 72)	72.2 % (26 of 36)	65.7 % (23 of 35)	100.0 % (1 of 1)
Methyl	85.1 % (97 of 114)	86.0 % (49 of 57)	84.2 % (48 of 57)

1. capsid protein of flavivirus

MNDQRKKARN TPFNMLKRER NRVSTVQQLT KRFSLGMLQG RGPLKLFMAL VAFLRFLTIP PTAGILKRWG TIKKSKAINV LRGFRKEIGR MLNILNRRRR

Show sample condition

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

LACS Plot; CA

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

Referencing offset: -0.56 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.56 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.77 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 1R6R, Strand ID: A, B Detail

Release date

2004-04-06

Citation

Solution structure of dengue virus capsid protein reveals another fold
Ma, L., Jones, C.T., Groesch, T.D., Kuhn, R.J., Post, C.B.
Proc. Natl. Acad. Sci. U. S. A. (2004), 101, 3414-3419, PubMed 14993605 , DOI 10.1073/pnas.0305892101 , Abstract

Related entities 1. Dengue type 2 virus capsid protein, : 1 : 1 : 6 : 31 entities Detail

Interaction partners 1. Dengue type 2 virus capsid protein, : 6 interactors Detail

More details for 6 interactors identified by 3 citations

Experiments performed 8 experiments Detail

1 HNCACB

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

2 CBCA(CO)NH

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

3 C(CO)NH

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

4 HC(CO)NH

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

5 HCCHTOCSY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

6 HSQC

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

7 hbCBcgcdHD

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

8 hbCBcgcdHDHE

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	capsid protein of flavivirus	[U-13C; U-15N]		1.6 mM

Sample #2

Temperature 300 (±1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	capsid protein of flavivirus	[U-15N]		2.0 ~ 4.0 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5973_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr5973_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	1116		97.0 (chain: 1, length: 100)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 100, Sequence coverage: 97.0%
- Total number of assignments
  - ¹³C chemical shifts: 394
  - ¹H chemical shifts: 618
  - ¹⁵N chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
68	ARG	HH11	6.215

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	485	394	81.2
¹H chemical shifts	686	509	74.2
¹⁵N chemical shifts	124	104	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	200	166	83.0
¹H chemical shifts	203	194	95.6
¹⁵N chemical shifts	96	91	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	285	228	80.0
¹H chemical shifts	483	315	65.2
¹⁵N chemical shifts	28	13	46.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	62	53	85.5
¹H chemical shifts	62	54	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	35	22	62.9
¹H chemical shifts	36	24	66.7
¹⁵N chemical shifts	1	1	100.0

Keywords NMR structure of flavivirus core protein

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Found 1 Document (0.952 seconds)

BMRB: 5973

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Dengue type 2 virus capsid protein, : 1 : 1 : 6 : 31 entities Detail

Interaction partners 1. Dengue type 2 virus capsid protein, : 6 interactors Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail