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BMRB: 16050

2KBM

Ca-S100A1 interacting with TRTK12

Authors

Wright, N.T., Varney, K.M., Cannon, B.R., Morgan, M., Weber, D.J.

Assembly

Ca-S100A1 and TRTK12

Entity

1. S100A1 (polymer, Thiol state: all free), 93 monomers, 10428.52 × 2 Da Detail

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKDLLQTE LSSFLDVQKD ADAVDKIMKE LDENGDGEVD FQEFVVLVAA LTVACNNFFW ENS

2. TRTK12 (polymer, Thiol state: all free), 12 monomers, 1474.703 × 2 Da Detail

TRTKIDWNKI LS

3. CA (non-polymer), 40.078 × 3 Da

Total weight

23926.68 Da

Max. entity weight

10428.52 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

simulated annealing, DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.3 %, Completeness (bb): 89.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.3 % (1015 of 1234)	85.7 % (546 of 637)	78.2 % (376 of 481)	80.2 % (93 of 116)
Backbone	89.5 % (564 of 630)	92.1 % (198 of 215)	88.1 % (273 of 310)	88.6 % (93 of 105)
Sidechain	76.7 % (540 of 704)	82.5 % (348 of 422)	70.8 % (192 of 271)	0.0 % (0 of 11)
Aromatic	10.0 % (10 of 100)	14.0 % (7 of 50)	6.3 % (3 of 48)	0.0 % (0 of 2)
Methyl	89.3 % (109 of 122)	95.1 % (58 of 61)	83.6 % (51 of 61)

1. S100A1

GSELETAMET LINVFHAHSG KEGDKYKLSK KELKDLLQTE LSSFLDVQKD ADAVDKIMKE LDENGDGEVD FQEFVVLVAA LTVACNNFFW ENS

2. TRTK12

TRTKIDWNKI LS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

Protein Blocks Logo

Calculated from 20 models in PDB: 2KBM, Strand ID: A, B, X, Y Detail

Release date

2009-04-03

Citation

Solution structure of S100A1 bound to the CapZ peptide (TRTK12)
Wright, N.T., Cannon, B.R., Wilder, P.T., Morgan, M.T., Varney, K.M., Zimmer, D.B., Weber, D.J.
J. Mol. Biol. (2009), 386, 1265-1277, PubMed 19452629 , DOI 10.1016/j.jmb.2009.01.022 , Abstract

Related entities 1. S100A1, : 1 : 84 entities Detail

Related entities 2. TRTK12, : 1 : 60 : 3 entities Detail

Interaction partners 2. TRTK12, : 6 interactors Detail

More details for 6 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

4 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

5 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

6 3D HNCO

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

7 3D HNCA

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

8 3D HNHA

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

9 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

10 IPAP-HSQC

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	D2O	natural abundance		10 %
2	H2O	natural abundance		90 %
3	CALCIUM ION	natural abundance		10 mM
4	DTT	natural abundance		10 mM
5	TRIS	natural abundance		10 mM
6	sodium chloride	natural abundance		25 mM
7	entity_1	[U-100% 13C; U-100% 15N]		500 uM
8	entity_2	natural abundance		1500 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16050_2kbm.nef
Input source #2: Coordindates	2kbm.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:OE2	5:1:CA:CA	unknown	unknown	n/a
3:62:ASP:OD2	5:2:CA:CA	unknown	unknown	n/a
3:66:ASP:OD1	5:2:CA:CA	unknown	unknown	n/a
3:68:GLU:O	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
4:32:GLU:OE2	5:3:CA:CA	unknown	unknown	n/a
4:62:ASP:OD2	5:4:CA:CA	unknown	unknown	n/a
4:66:ASP:OD1	5:4:CA:CA	unknown	unknown	n/a
4:68:GLU:O	5:4:CA:CA	unknown	unknown	n/a
4:73:GLU:OE2	5:4:CA:CA	unknown	unknown	n/a
3:32:GLU:OE1	5:1:CA:CA	unknown	unknown	n/a
3:62:ASP:OD1	5:2:CA:CA	unknown	unknown	n/a
3:73:GLU:OE1	5:2:CA:CA	unknown	unknown	n/a
4:32:GLU:OE1	5:3:CA:CA	unknown	unknown	n/a
4:62:ASP:OD1	5:4:CA:CA	unknown	unknown	n/a
4:73:GLU:OE1	5:4:CA:CA	unknown	unknown	n/a
3:61:LEU:O	5:2:CA:CA	unknown	unknown	n/a
4:61:LEU:O	5:4:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None
C	3	CA	CALCIUM ION	None
C	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): X vs Auth_asym_ID (model): Y
Entity_assembly_ID (NMR): Y vs Auth_asym_ID (model): X

Chain assignments

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

Content subtype: combined_16050_2kbm.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_1	Warning	1008		100.0 (chain: A, length: 93), 100.0 (chain: X, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4566 (1)	noe	98.9 (chain: A, length: 93), 98.9 (chain: B, length: 93), 100.0 (chain: X, length: 12), 100.0 (chain: Y, length: 12)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	276 (276)	.	92.5 (chain: A, length: 93), 92.5 (chain: B, length: 93), 58.3 (chain: X, length: 12), 58.3 (chain: Y, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	250 (250)	.	86.0 (chain: A, length: 93), 86.0 (chain: B, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
  - Entity_assembly_ID: X, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 546
  - ¹³C chemical shifts: 369
  - ¹⁵N chemical shifts: 93
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: X
- Redox state of CYS
- 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: X

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 98.9%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 98.9%
  - Entity_assembly_ID: X, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: Y, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 4566
- Weight of restraints: 1.0 (4566)
- Potential type of restraints: square-well-parabolic (4566)
- Range of distance target values: 2.25, 4.0 (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
    None
  - Chain_ID: X
  - Chain_ID: Y
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 92.5%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 92.5%
  - Entity_assembly_ID: X, Chain length: 12, Sequence coverage: 58.3%
  - Entity_assembly_ID: Y, Chain length: 12, Sequence coverage: 58.3%
- Total number of restraints: 276
- Total number of restraints per polymer type: 276
- Weight of restraints: 1.0 (276)
- Potential type of restraints: square-well-parabolic (276)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: X
  - Chain_ID: Y

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 86.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 ||||||||||||||||||||| ||||||||||||||||||| ||| ||  |||||||||||||||||||||||||||| |||||     || 
.SELETAMETLINVFHAHSGKE.DKYKLSKKELKDLLQTELS.FLD.QK..DAVDKIMKELDENGDGEVDFQEFVVLVA.LTVAC.....EN 
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 86.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90---
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
 ||||||||||||||||||||| ||||||||||||||||||| ||| ||  |||||||||||||||||||||||||||| |||||     || 
.SELETAMETLINVFHAHSGKE.DKYKLSKKELKDLLQTELS.FLD.QK..DAVDKIMKELDENGDGEVDFQEFVVLVA.LTVAC.....EN 
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Total number of restraints: 250
Potential type of restraints: undefined (250)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords CapZ, conformational change, EF-hand, Protein-protein interaction, S100