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BMRB: 19604

2MGU

1H, 13C, and 15N chemical shift assignments for the complex of calmodulin with minimal binding domain from HIV-1 matrix protein

Authors

Vlach, J., Samal, A., Saad, J.

Assembly

complex of calmodulin with minimal binding domain from HIV-1 matrix protein

Entity

1. calmodulin (polymer, Thiol state: not present), 148 monomers, 16706.21 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. MA8-43 (polymer, Thiol state: not present), 36 monomers, 4305.982 Da Detail

LSGGELDKWE KIRLRPGGKK QYKLKHIVWA SRELER

3. CALCIUM ION (non-polymer), 40.078 × 4 Da

Total weight

21172.506 Da

Max. entity weight

16706.21 Da

Source organism

Rattus norvegicus , Human immunodeficiency virus 1

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 87.9 %, Completeness (bb): 84.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.9 % (1876 of 2134)	93.3 % (1042 of 1117)	78.8 % (647 of 821)	95.4 % (187 of 196)
Backbone	84.2 % (924 of 1098)	95.0 % (361 of 380)	72.6 % (390 of 537)	95.6 % (173 of 181)
Sidechain	92.4 % (1114 of 1205)	92.4 % (681 of 737)	92.5 % (419 of 453)	93.3 % (14 of 15)
Aromatic	95.6 % (130 of 136)	95.6 % (65 of 68)	95.5 % (63 of 66)	100.0 % (2 of 2)
Methyl	94.9 % (167 of 176)	92.0 % (81 of 88)	97.7 % (86 of 88)

1. calmodulin

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. MA8-43

LSGGELDKWE KIRLRPGGKK QYKLKHIVWA SRELER

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MGU, Strand ID: A, M Detail

Release date

2013-11-11

Citation

Solution structure of calmodulin bound to the binding domain of the HIV-1 matrix protein
Vlach, J., Samal, A.B., Saad, J.S.
J. Biol. Chem. (2014), 289, 8697-8705, PubMed 24500712 , DOI 10.1074/jbc.M113.543694 , Abstract

Related entities 1. calmodulin, : 11 : 88 entities Detail

Related entities 2. MA8-43, : 1 : 17 : 31 : 1 : 73 entities Detail

Interaction partners 2. MA8-43, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

3 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

6 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-95% 13C; U-95% 15N]		0.1 ~ 1.2 mM
2	MA8-43	natural abundance		0.1 ~ 1.2 mM
3	CALCIUM ION	natural abundance		5 mM
4	D2O	natural abundance		100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19604_2mgu.nef
Input source #2: Coordindates	2mgu.cif
Diamagnetism of the molecular assembly	False (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)
1:133:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:20:ASP:OD1	3:3:CA:CA	unknown	unknown	n/a
1:67:GLU:OE1	3:4:CA:CA	unknown	unknown	n/a
1:131:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:31:GLU:OE2	3:3:CA:CA	unknown	unknown	n/a
1:140:GLU:OE2	3:2:CA:CA	unknown	unknown	n/a
1:24:ASP:OD1	3:3:CA:CA	unknown	unknown	n/a
1:67:GLU:OE2	3:4:CA:CA	unknown	unknown	n/a
1:31:GLU:OE1	3:3:CA:CA	unknown	unknown	n/a
1:99:TYR:O	3:1:CA:CA	unknown	unknown	n/a
1:60:ASN:OD1	3:4:CA:CA	unknown	unknown	n/a
1:140:GLU:OE1	3:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a
1:104:GLU:OE2	3:1:CA:CA	unknown	unknown	n/a
1:93:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:95:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:104:GLU:OE1	3:1:CA:CA	unknown	unknown	n/a
1:26:THR:O	3:3:CA:CA	unknown	unknown	n/a
1:97:ASN:OD1	3:1:CA:CA	unknown	unknown	n/a
1:22:ASP:OD1	3:3:CA:CA	unknown	unknown	n/a
1:135:GLN:O	3:2:CA:CA	unknown	unknown	n/a
1:62:THR:O	3:4:CA:CA	unknown	unknown	n/a
1:56:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a
1:129:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:131:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:133:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None
B	2	CA	CALCIUM ION	None
B	3	CA	CALCIUM ION	None
B	4	CA	CALCIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
||||||||||||||||||||||||||||||||||||||||||||||||
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0
M	M	36	0	0	100.0

Content subtype: combined_19604_2mgu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	26		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1888		98.6 (chain: A, length: 148), 100.0 (chain: M, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	331 (1)	noe	24.3 (chain: A, length: 148), 63.9 (chain: M, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 98.6%
  - Entity_assembly_ID: M, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1059
  - ¹³C chemical shifts: 632
  - ¹⁵N chemical shifts: 197
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: M
- Peptide bond of PRO
- Tautomeric state of HIS
- 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
  - Chain_ID: M

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 24.3%
  - Entity_assembly_ID: M, Chain length: 36, Sequence coverage: 63.9%
- Total number of restraints: 328
- Weight of restraints: 1.0 (328)
- Potential type of restraints: upper-bound-parabolic (328)
- Range of distance target values: 0.0, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: M
- Distance restraints on contact map

Keywords HIV-1 matrix, calmodulin