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BMRB: 30798

7KRB

Solution Structure of the Dysferlin C2A Domain in its Calcium-free State

Authors

Wang, Y., Mercier, P., Santamaria, L., Shaw, G.S.

Assembly

Isoform 15 of Dysferlin

Entity

1. Isoform 15 of Dysferlin (polymer), 138 monomers, 14805.76 Da Detail

GSGGGGGMLR VFILYAENVH TPDTDISDAY CSAVFAGVKK RTKVIKNSVN PVWNEGFEWD LKGIPLDQGS ELHVVVKDHE TMGRNRFLGE AKVPLREVLA TPSLSASFNA PLLDTKKQPT GASLVLQVSY TPLPGAVL

Formula weight

14805.76 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.1 %, Completeness: 68.4 %, Completeness (bb): 68.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.4 % (1072 of 1567)	74.7 % (601 of 805)	57.5 % (355 of 617)	80.0 % (116 of 145)
Backbone	68.9 % (558 of 810)	80.8 % (227 of 281)	56.5 % (226 of 400)	81.4 % (105 of 129)
Sidechain	70.0 % (617 of 881)	71.4 % (374 of 524)	68.0 % (232 of 341)	68.8 % (11 of 16)
Aromatic	19.1 % (21 of 110)	34.5 % (19 of 55)	0.0 % (0 of 53)	100.0 % (2 of 2)
Methyl	85.5 % (147 of 172)	87.2 % (75 of 86)	83.7 % (72 of 86)

1. entity 1

GSGGGGGMLR VFILYAENVH TPDTDISDAY CSAVFAGVKK RTKVIKNSVN PVWNEGFEWD LKGIPLDQGS ELHVVVKDHE TMGRNRFLGE AKVPLREVLA TPSLSASFNA PLLDTKKQPT GASLVLQVSY TPLPGAVL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		1 mM
8	MES	natural abundance		25 mM
9	NaCl	natural abundance		150 mM
10	EDTA	natural abundance		5 mM
11	DTT	natural abundance		1 mM
12	Protein	[U-13C; U-15N]		0.3 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 7K6B, Strand ID: A Detail

Release date

2020-10-18

Citation

Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner
Wang, Y., Tadayon, R., Santamaria, L., Mercier, P., Forristal, C.J., Shaw, G.S.
Biochem. J. (2021), 478, 197-215, PubMed 33449082 , DOI 10.1042/BCJ20200773 , Abstract

Related entities 1. Isoform 15 of Dysferlin, : 1 : 1 : 4 : 59 entities Detail

Interaction partners 1. Isoform 15 of Dysferlin, : 44 interactors Detail

More details for 44 interactors identified by 3 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		1 mM
8	MES	natural abundance		25 mM
9	NaCl	natural abundance		150 mM
10	EDTA	natural abundance		5 mM
11	DTT	natural abundance		1 mM
12	Protein	[U-13C; U-15N]		0.3 mM

3 3D HNCO

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

6 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

8 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

10 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		1 mM
8	MES	natural abundance		25 mM
9	NaCl	natural abundance		150 mM
10	EDTA	natural abundance		5 mM
11	DTT	natural abundance		1 mM
12	Protein	[U-13C; U-15N]		0.3 mM

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		1 mM
8	MES	natural abundance		25 mM
9	NaCl	natural abundance		150 mM
10	EDTA	natural abundance		5 mM
11	DTT	natural abundance		1 mM
12	Protein	[U-13C; U-15N]		0.3 mM

12 3D HNCA

Instrument

Varian INOVA - 600 MHz cold-probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 5.5, Details 1 mM DSS, 25 mM MES, 150 mM NaCl, 5 mM EDTA, 1 mM DTT, 0.3 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		1 mM
2	MES	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	EDTA	natural abundance		5 mM
5	DTT	natural abundance		1 mM
6	Protein	[U-13C; U-15N]		0.3 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30798_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: bmr30798_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1192		88.4 (chain: 1, length: 138)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 138, Sequence coverage: 88.4%
- Total number of assignments
  - ¹H chemical shifts: 746
  - ¹⁵N chemical shifts: 114
  - ¹³C chemical shifts: 332
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords MEMBRANE PROTEIN, beta-sandwich, calcium-binding, membrane repair