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Found 1 Document (0.502 seconds)

BMRB: 19857

2MMK

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, 8417.969 Da Detail

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWXPEELL XDGEDDVFDP DLDMEVVFET Q

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

Total weight

8483.378 Da

Max. entity weight

8417.969 Da

Entity Connection

metal coordination 2 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

Source organism

Mengo virus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 51.2 %, Completeness (bb): 66.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	51.2 % (404 of 789)	41.5 % (169 of 407)	54.7 % (170 of 311)	91.5 % (65 of 71)
Backbone	66.2 % (270 of 408)	51.4 % (71 of 138)	66.2 % (135 of 204)	97.0 % (64 of 66)
Sidechain	44.5 % (199 of 447)	36.4 % (98 of 269)	57.8 % (100 of 173)	20.0 % (1 of 5)
Aromatic	10.0 % (8 of 80)	10.0 % (4 of 40)	10.3 % (4 of 39)	0.0 % (0 of 1)
Methyl	86.2 % (50 of 58)	86.2 % (25 of 29)	86.2 % (25 of 29)

1. entity 1

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWXPEELL XDGEDDVFDP DLDMEVVFET Q

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4, Details L MENGO TREATED WITH CK2 AND SYK. BUFFER: 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 2P	[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: 2MMK, 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

Entries sharing articles BMRB: 4 entries Detail

  BMRB: 19854 released on 2014-10-06
    Title Structural Characterization of the Mengovirus Leader Protein Bound to Ran GTPase by Nuclear Magnetic Resonance
  BMRB: 19855 released on 2014-10-06
    Title Structural Characterization of the Mengovirus Leader Protein Bound to Ran GTPase by Nuclear Magnetic Resonance
  BMRB: 19858 released on 2014-10-06
    Title NMR Studies of the Phosphorylation of the Mengovirus Leader Protein Reveal Stabilization of Intermolecular Domain Interactions
  BMRB: 19084 released on 2013-04-16
    Title The Mengovirus Leader protein

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, Temperature 298 K, pH 7.4, Details L MENGO TREATED WITH CK2 AND SYK. BUFFER: 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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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 2P	[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_19857_2mmk.nef
Input source #2: Coordindates	2mmk.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)
1:44:TRP:C	1:45:PTR:N	unknown	unknown	n/a
1:45:PTR:C	1:46:PRO:N	unknown	unknown	n/a
1:50:LEU:C	1:51:TPO:N	unknown	unknown	n/a
1:51:TPO:C	1:52:ASP:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	45	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Torsion angle restraints, Coordinates
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-
GSTAMATTMEQEICAHSMTFEECPKCSALQYRNGFYLLKYDEEWXPEELLXDGEDDVFDPDLDMEVVFETQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSTAMATTMEQEICAHSMTFEECPKCSALQYRNGFYLLKYDEEWXPEELLXDGEDDVFDPDLDMEVVFETQ

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_19857_2mmk.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	387		97.2 (chain: A, length: 71)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	88 (88)	.	93.0 (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: 159
  - ¹³C chemical shifts: 159
  - 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	130.719
46	PRO	N	106.719
60	PRO	N	131.844

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	419	159	37.9
¹³C chemical shifts	322	159	49.4
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	92	33.2
¹³C chemical shifts	180	97	53.9
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	26	76.5
¹³C chemical shifts	34	26	76.5

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: 93.0%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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

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Found 1 Document (0.502 seconds)

BMRB: 19857

Sample

Entries sharing articles BMRB: 4 entries Detail

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