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Found 1 Document (0.561 seconds)

BMRB: 19858

2MML

NMR Studies of the Phosphorylation of the Mengovirus Leader Protein Reveal Stabilization of Intermolecular Domain Interactions

Authors

Bacot-Davis, V.R., Porter, F.W., Palmenberg, A.C.

Assembly

Phosphorylated Mengovirus Leader Protein

Entity

1. Phosphorylated Mengovirus Leader Protein, entity 1 (polymer), 71 monomers, 8337.990 Da Detail

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWYPEELL XDGEDDVFDP DLDMEVVFET Q

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

Total weight

8403.399 Da

Max. entity weight

8337.99 Da

Entity Connection

metal coordination 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS14:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS23:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS26:SG	2:ZN1:ZN

Source organism

Mengo virus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 48.6 %, Completeness (bb): 64.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	48.6 % (391 of 805)	39.3 % (163 of 415)	51.3 % (163 of 318)	90.3 % (65 of 72)
Backbone	64.0 % (265 of 414)	49.3 % (69 of 140)	63.3 % (131 of 207)	97.0 % (65 of 67)
Sidechain	41.7 % (191 of 458)	34.2 % (94 of 275)	54.5 % (97 of 178)	0.0 % (0 of 5)
Aromatic	0.0 % (0 of 88)	0.0 % (0 of 44)	0.0 % (0 of 43)	0.0 % (0 of 1)
Methyl	89.7 % (52 of 58)	86.2 % (25 of 29)	93.1 % (27 of 29)

1. entity 1

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWYPEELL XDGEDDVFDP DLDMEVVFET Q

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details L MENGO TREATED WITH CK2. 20mM HEPES, pH 7.4, 100mM KCl (99.9% purity), 2mM MgCl2 (99.9% purity), 2mM DTT, 0.04% NaN3

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MML, Strand ID: A Detail

Release date

2014-10-06

Citation

Solution structures of Mengovirus Leader protein, its phosphorylated derivatives, and in complex with nuclear transport regulatory protein, RanGTPase
Bacot-Davis, V.R., Ciomperlik, J.J., Basta, H.A., Cornilescu, C.C., Palmenberg, A.C.
Proc. Natl. Acad. Sci. U. S. A. (2014), 111, 15792-15797, PubMed 25331866 , DOI 10.1073/pnas.1411098111 , Abstract

Related entities 1. Phosphorylated Mengovirus Leader Protein, entity 1, : 1 : 5 : 5 entities Detail

Interaction partners 1. Phosphorylated Mengovirus Leader Protein, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details L MENGO TREATED WITH CK2. 20mM HEPES, pH 7.4, 100mM KCl (99.9% purity), 2mM MgCl2 (99.9% purity), 2mM DTT, 0.04% NaN3

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 31-P

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	L MENGO 1P	[U-100% 13C; U-100% 15N]	0.5 mM
2	HEPES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	magnesium chloride	natural abundance	2 mM
5	DTT	natural abundance	2 mM
6	sodium azide	natural abundance	0.04 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_19858_2mml.nef
Input source #2: Coordindates	2mml.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	Warning

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)
1:50:LEU:C	1:51:TPO:N	unknown	unknown	n/a
1:51:TPO:C	1:52:ASP:N	unknown	unknown	n/a
1:14:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	51	TPO	PHOSPHOTHREONINE	Assigned chemical shifts, Coordinates
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70-
GSTAMATTMEQEICAHSMTFEECPKCSALQYRNGFYLLKYDEEWYPEELLXDGEDDVFDPDLDMEVVFETQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSTAMATTMEQEICAHSMTFEECPKCSALQYRNGFYLLKYDEEWYPEELLXDGEDDVFDPDLDMEVVFETQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	71	0	0	100.0

Content subtype: combined_19858_2mml.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	390		97.2 (chain: A, length: 71)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	87 (87)	.	88.7 (chain: A, length: 71)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 160
  - ¹³C chemical shifts: 161
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
24	PRO	N	105.719
46	PRO	N	133.469
60	PRO	N	128.594

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	419	160	38.2
¹³C chemical shifts	322	161	50.0
¹⁵N chemical shifts	74	66	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	67	47.2
¹³C chemical shifts	142	62	43.7
¹⁵N chemical shifts	68	66	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	93	33.6
¹³C chemical shifts	180	99	55.0
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	25	73.5
¹³C chemical shifts	34	27	79.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	0	0.0
¹³C chemical shifts	43	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 88.7%
- Total number of restraints: 87
- Total number of restraints per polymer type: 87
- Weight of restraints: 1.0 (87)
- Potential type of restraints: square-well-parabolic (87)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANIMAL VIRUSES, CARDIOVIRUSES, CASEIN KINASE 2, LEADER, MENGOVIRUS, PHOSPHORYLATION, POSITIVE-STRAND RNA VIRUSES, PROTEIN PHOSPHORYLATION

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Found 1 Document (0.561 seconds)

BMRB: 19858

Sample

Related entities 1. Phosphorylated Mengovirus Leader Protein, entity 1, : 1 : 5 : 5 entities Detail

Interaction partners 1. Phosphorylated Mengovirus Leader Protein, entity 1, : 1 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail