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BMRB: 15704

2K2F

Ca2+-S100A1-RyRP12

Authors

Wright, N.T., Varney, K.M., Weber, D.J.

Assembly

S100A1 bound to calmodulin

Entity

1. S100A1 (polymer, Thiol state: not present), 12 monomers, 1465.781 × 2 Da Detail

KKAVWHKLLS KQ

2. calmodulin (polymer, Thiol state: all free), 93 monomers, 10428.52 × 2 Da Detail

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKDLLQTE LSSFLDVQKD ADAVDKIMKE LDENGDGEVD FQEFVVLVAA LTVACNNFFW ENS

3. CA (non-polymer), 40.078 × 3 Da

Total weight

23908.836 Da

Max. entity weight

10428.52 Da

Source organism

Rattus norvegicus , Homo sapiens

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 15.2 %, Completeness: 12.7 %, Completeness (bb): 10.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	12.7 % (97 of 761)	13.6 % (88 of 645)	7.8 % (9 of 116)
Backbone	10.6 % (34 of 320)	11.6 % (25 of 215)	8.6 % (9 of 105)
Sidechain	14.3 % (63 of 441)	14.7 % (63 of 430)	0.0 % (0 of 11)
Aromatic	7.4 % (4 of 54)	7.7 % (4 of 52)	0.0 % (0 of 2)
Methyl	11.7 % (7 of 60)	11.7 % (7 of 60)

1. S100A1

KKAVWHKLLS KQ

2. calmodulin

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKDLLQTE LSSFLDVQKD ADAVDKIMKE LDENGDGEVD FQEFVVLVAA LTVACNNFFW ENS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2K2F, Strand ID: A, B, C, D Detail

Release date

2008-08-27

Citation

S100A1 and calmodulin compete for the same binding site on ryanodine receptor
Wright, N.T., Prosser, B.L., Varney, K.M., Zimmer, D.B., Schneider, M.F., Weber, D.J.
J. Biol. Chem. (2008), 283, 26676-26683, PubMed 18650434 , DOI 10.1074/jbc.M804432200 , Abstract

Related entities 1. S100A1, : 1 : 20 entities Detail

Related entities 2. calmodulin, : 1 : 84 entities Detail

Interaction partners 1. S100A1, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker DMX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

4 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

8 3D 13C ed 12C filt NOESY

Instrument

Bruker DMX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2, Details S100A1-RyRP12 solution for NMR

#	Name	Isotope labeling	Type	Concentration
1	CALCIUM ION	natural abundance		10-15 mM
2	entity_1	[U-100% 13C; U-100% 15N]		1-3 mM
3	entity_2	natural abundance		2-6 mM
4	D2O	natural abundance		10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15704_2k2f.nef
Input source #2: Coordindates	2k2f.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)
3:19:SER:O	5:1:CA:CA	unknown	unknown	n/a
3:24:ASP:N	5:1:CA:CA	unknown	unknown	n/a
3:24:ASP:O	5:1:CA:CA	unknown	unknown	n/a
3:27:LYS:O	5:1:CA:CA	unknown	unknown	n/a
3:32:GLU:OE1	5:1:CA:CA	unknown	unknown	n/a
3:32:GLU:OE2	5:1:CA:CA	unknown	unknown	n/a
3:62:ASP:OD1	5:2:CA:CA	unknown	unknown	n/a
3:66:ASP:OD2	5:2:CA:CA	unknown	unknown	n/a
3:68:GLU:O	5:2:CA:CA	unknown	unknown	n/a
3:73:GLU:OE1	5:2:CA:CA	unknown	unknown	n/a
3:73:GLU:OE2	5:2:CA:CA	unknown	unknown	n/a
4:19:SER:O	5:3:CA:CA	unknown	unknown	n/a
4:24:ASP:N	5:3:CA:CA	unknown	unknown	n/a
4:24:ASP:O	5:3:CA:CA	unknown	unknown	n/a
4:27:LYS:O	5:3:CA:CA	unknown	unknown	n/a
4:62:ASP:OD1	5:4:CA:CA	unknown	unknown	n/a
4:66:ASP:OD2	5:4:CA:CA	unknown	unknown	n/a
4:68:GLU:O	5:4:CA:CA	unknown	unknown	n/a
4:73:GLU:OE1	5:4:CA:CA	unknown	unknown	n/a
4:73:GLU:OE2	5:4:CA:CA	unknown	unknown	n/a

Non-standard residues

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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A
Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B
Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C
Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
C	C	12	0	0	100.0
D	D	12	0	0	100.0
A	A	93	0	0	100.0
B	B	93	0	0	100.0

Content subtype: combined_15704_2k2f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	20		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	84		100.0 (chain: C, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4520 (1)	noe	100.0 (chain: A, length: 93), 100.0 (chain: B, length: 93), 100.0 (chain: C, length: 12), 100.0 (chain: D, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	172 (1)	hbond	63.4 (chain: A, length: 93), 63.4 (chain: B, length: 93)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	278 (278)	.	89.2 (chain: A, length: 93), 89.2 (chain: B, length: 93), 75.0 (chain: C, length: 12), 75.0 (chain: D, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	116 (116)	.	62.4 (chain: A, length: 93), 62.4 (chain: B, length: 93)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	118 (118)	.	63.4 (chain: A, length: 93), 62.4 (chain: B, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 77
  - ¹⁵N chemical shifts: 7
- Completeness of assignments
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: C

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 4513
- Weight of restraints: 1.0 (4513)
- Potential type of restraints: square-well-parabolic (4513)
- Range of distance target values: 2.35, 23.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 63.4%
    - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 63.4%
  - Total number of restraints: 172
  - Weight of restraints: 1.0 (172)
  - Potential type of restraints: square-well-parabolic (172)
  - Range of distance target values: 2.6, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
    - Chain_ID: D
      None
    - Chain_ID: E
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 89.2%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 89.2%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 75.0%
  - Entity_assembly_ID: D, Chain length: 12, Sequence coverage: 75.0%
- Total number of restraints: 278
- Total number of restraints per polymer type: 278
- Weight of restraints: 1.0 (278)
- Potential type of restraints: square-well-parabolic (278)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 62.4%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 |||  |  || ||  |||||| ||||||| ||| ||||   || |||   |||| | ||| || || | |   ||| |||||||       |
.SEL..A..TL.NV..AHSGKE.DKYKLSK.ELK.LLQT...SF.DVQ...DAVD.I.KEL.EN.DG.V.F...VVL.AALTVAC.......S

Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 62.4%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 |||  |  || ||  |||||| ||||||| ||| ||||   || |||   |||| | ||| || || | |   ||| |||||||       |
.SEL..A..TL.NV..AHSGKE.DKYKLSK.ELK.LLQT...SF.DVQ...DAVD.I.KEL.EN.DG.V.F...VVL.AALTVAC.......S

Total number of restraints: 116
Potential type of restraints: undefined (116)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Saveframe: CNS/XPLOR_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 63.4%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 |||||| ||||||| ||| |    ||| |||  | ||| ||  ||    |||||||||||||| | ||| || | ||| ||     |   | 
.SELETA.ETLINVF.AHS.K....YKL.KKE..D.LQT.LS..LD....ADAVDKIMKELDEN.D.EVD.QE.V.LVA.LT.....F...N 
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 62.4%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 || ||| ||||||| ||| |    ||| |||  | ||| ||  ||    |||||||||||||| | ||| || | ||| ||     |   | 
.SE.ETA.ETLINVF.AHS.K....YKL.KKE..D.LQT.LS..LD....ADAVDKIMKELDEN.D.EVD.QE.V.LVA.LT.....F...N 
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Total number of restraints: 118
Potential type of restraints: undefined (118)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords calcium binding, EF hand, ryanodine receptor, S100