BMRBj - BMREntryMaster

Found 1 Document (0.446 seconds)

BMRB: 19855

2MMI

Structural Characterization of the Mengovirus Leader Protein Bound to Ran GTPase by Nuclear Magnetic Resonance

Authors

Bacot-Davis, V.R., Cornilescu, C.C., Markley, J.L., Palmenberg, A.C.

Assembly

Mengovirus Leader Protein Bound to Ran GTPase

Entity

1. Mengovirus Leader Protein Bound to Ran GTPase, entity 1 (polymer, Thiol state: all free), 71 monomers, 8258.010 Da Detail

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWYPEELL TDGEDDVFDP DLDMEVVFET Q

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

Total weight

8323.419 Da

Max. entity weight

8258.01 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: 98.6 %, Completeness: 50.7 %, Completeness (bb): 65.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.7 % (413 of 814)	41.3 % (173 of 419)	53.7 % (173 of 322)	91.8 % (67 of 73)
Backbone	65.7 % (276 of 420)	50.0 % (71 of 142)	65.7 % (138 of 210)	98.5 % (67 of 68)
Sidechain	43.9 % (203 of 462)	36.8 % (102 of 277)	56.1 % (101 of 180)	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	90.0 % (54 of 60)	90.0 % (27 of 30)	90.0 % (27 of 30)

1. entity 1

GSTAMATTME QEICAHSMTF EECPKCSALQ YRNGFYLLKY DEEWYPEELL TDGEDDVFDP DLDMEVVFET Q

Show sample condition

Sample

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

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

Protein Blocks Logo

Calculated from 10 models in PDB: 2MMI, 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. Mengovirus Leader Protein Bound to Ran GTPase, entity 1, : 1 : 2 : 3 : 5 entities Detail

Interaction partners 1. Mengovirus Leader Protein Bound to Ran GTPase, 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 TITRATED WITH RAN GTPASE. BUFFER:20mM HEPES (pH 7.4), 100mM KCl (99.9% purity), 2mM MgCl2 (99.9% purity), 2mM DTT, and 0.04% NaN3

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

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

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

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

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

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

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

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

10 31-P

Instrument

Bruker Avance - 600 MHz

Sample

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

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_19855_2mmi.nef
Input source #2: Coordindates	2mmi.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)
1:23:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:1: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

Sequence alignments

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

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

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_19855_2mmi.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	389		98.6 (chain: A, length: 71)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	91 (91)	.	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: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 160
  - ¹³C chemical shifts: 159
  - ¹⁵N chemical shifts: 70
- 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	103.516
46	PRO	N	98.633
60	PRO	N	95.898

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	419	160	38.2
¹³C chemical shifts	322	159	49.4
¹⁵N chemical shifts	74	67	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	68	47.9
¹³C chemical shifts	142	61	43.0
¹⁵N chemical shifts	68	67	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	92	33.2
¹³C chemical shifts	180	98	54.4
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	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: 93.0%
- Total number of restraints: 91
- Total number of restraints per polymer type: 91
- Weight of restraints: 1.0 (91)
- Potential type of restraints: square-well-parabolic (91)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANIMAL VIRUSES, CARDIOVIRUSES, LEADER, NUCLEOCYTOPLASMIC TRANSPORT, POSITIVE-STRAND RNA VIRUSES

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Found 1 Document (0.446 seconds)

BMRB: 19855

Sample

Related entities 1. Mengovirus Leader Protein Bound to Ran GTPase, entity 1, : 1 : 2 : 3 : 5 entities Detail

Interaction partners 1. Mengovirus Leader Protein Bound to Ran GTPase, entity 1, : 1 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail