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Found 1 Document (6.419 seconds)

BMRB: 15418

2JTT

NMR structure of the S100A6 dimer in complex with a binding fragment of the Siah-1 interacting protein

Authors

Lee, Y., Chazin, W.J.

Assembly

Complex of S100A6 and SIP(189-219)

Entity

1. S100A6 (polymer, Thiol state: not present), 90 monomers, 10153.61 × 2 Da Detail

MASPLDQAIG LLIGIFHKYS GKEGDKHTLS KKELKELIQK ELTIGSKLQD AEIVKLMDDL DRNKDQEVNF QEYITFLGAL AMIYNEALKG

2. SIP(189-219) (polymer, Thiol state: not present), 35 monomers, 3940.375 × 2 Da Detail

GPGSSEGLMN VLKKIYEDGD DDMKRTINKA WVESR

Total weight

28187.97 Da

Max. entity weight

10153.61 Da

Source organism

Oryctolagus cuniculus , Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 52.8 %, Completeness (bb): 71.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.8 % (785 of 1486)	46.7 % (364 of 780)	53.5 % (306 of 572)	85.8 % (115 of 134)
Backbone	71.7 % (535 of 746)	66.0 % (171 of 259)	69.8 % (254 of 364)	89.4 % (110 of 123)
Sidechain	41.5 % (354 of 854)	37.0 % (193 of 521)	48.4 % (156 of 322)	45.5 % (5 of 11)
Aromatic	23.2 % (19 of 82)	24.4 % (10 of 41)	20.0 % (8 of 40)	100.0 % (1 of 1)
Methyl	34.8 % (48 of 138)	37.7 % (26 of 69)	31.9 % (22 of 69)

1. S100A6

MASPLDQAIG LLIGIFHKYS GKEGDKHTLS KKELKELIQK ELTIGSKLQD AEIVKLMDDL DRNKDQEVNF QEYITFLGAL AMIYNEALKG

2. SIP(189-219)

GPGSSEGLMN VLKKIYEDGD DDMKRTINKA WVESR

Show sample condition

Sample #1

Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains double-labeled SIP(189-219) and unlabeled S100A6. 2% TFE(trifluoroethanol) was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
1	SIP(189-219)	[U-100% 13C; U-100% 15N]	1 mM
2	S100A6	natural abundance	1 mM
3	TRIS	[U-2H]	0.05 mM
4	Ca2+	natural abundance	0.01 mM
5	H2O		93 %
6	D2O		5 %
7	d-TFE		2 %

Sample #2

Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 15N-labeled SIP(189-219) and unlabeled S100A6. 2% d-TFE was added to improve spectral quality

#	Name	Isotope labeling	Concentration
8	SIP(189-219)	[U-100% 15N]	1 mM
9	S100A6	natural abundance	1 mM
10	TRIS	[U-2H]	0.05 mM
11	Ca2+	natural abundance	0.01 mM
12	H2O		93 %
13	D2O		5 %
14	d-TFE		2 %

Sample #3

Solvent system 98% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 13C-labeled SIP(189-219) and unlabeled S100A6. 2% d-TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
15	SIP(189-219)	[U-100% 13C]	1 mM
16	S100A6	natural abundance	1 mM
17	TRIS	[U-2H]	0.05 mM
18	Ca2+	natural abundance	0.01 mM
19	D2O		98 %
20	d-TFE		2 %

Sample #4

Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 13C-labeled SIP(189-219) and 15N-labeled S100A6. 2% TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
21	SIP(189-219)	[U-100% 13C]	2.3 mM
22	S100A6	[U-100% 15N]	2.3 mM
23	TRIS	[U-2H]	0.05 mM
24	Ca2+	natural abundance	0.01 mM
25	H2O		93 %
26	D2O		5 %
27	d-TFE		2 %

Sample #5

Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains unlabeled SIP(189-219) and double-labeled S100A6. 2% TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
28	SIP(189-219)	natural abundance	1 mM
29	S100A6	[U-100% 13C; U-100% 15N]	1 mM
30	TRIS	[U-2H]	0.05 mM
31	Ca2+	natural abundance	0.01 mM
32	H2O		93 %
33	D2O		5 %
34	d-TFE		2 %

Protein Blocks Logo

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

Release date

2008-10-28

Citation

Structure of the S100A6 complex with a fragment from the C-terminal domain of Siah-1 interacting protein: a novel mode for S100 protein target recognition
Lee, Y., Dimitrova, Y.N., Schneider, G., Ridenour, W.B., Bhattacharya, S., Soss, S.E., Caprioli, R.M., Filipek, A., Chazin, W.J.
Biochemistry (2008), 47, 10921-10932, PubMed 18803400 , DOI 10.1021/bi801233z , Abstract

Related entities 1. S100A6, : 71 entities Detail

Related entities 2. SIP(189-219), : 1 : 9 : 34 entities Detail

Interaction partners 2. SIP(189-219), : 20 interactors Detail

More details for 20 interactors identified by 4 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 15N-labeled SIP(189-219) and unlabeled S100A6. 2% d-TFE was added to improve spectral quality

#	Name	Isotope labeling	Concentration
8	SIP(189-219)	[U-100% 15N]	1 mM
9	S100A6	natural abundance	1 mM
10	TRIS	[U-2H]	0.05 mM
11	Ca2+	natural abundance	0.01 mM
12	H2O		93 %
13	D2O		5 %
14	d-TFE		2 %

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
8	SIP(189-219)	[U-100% 15N]	1 mM
9	S100A6	natural abundance	1 mM
10	TRIS	[U-2H]	0.05 mM
11	Ca2+	natural abundance	0.01 mM
12	H2O		93 %
13	D2O		5 %
14	d-TFE		2 %

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains double-labeled SIP(189-219) and unlabeled S100A6. 2% TFE(trifluoroethanol) was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
1	SIP(189-219)	[U-100% 13C; U-100% 15N]	1 mM
2	S100A6	natural abundance	1 mM
3	TRIS	[U-2H]	0.05 mM
4	Ca2+	natural abundance	0.01 mM
5	H2O		93 %
6	D2O		5 %
7	d-TFE		2 %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SIP(189-219)	[U-100% 13C; U-100% 15N]	1 mM
2	S100A6	natural abundance	1 mM
3	TRIS	[U-2H]	0.05 mM
4	Ca2+	natural abundance	0.01 mM
5	H2O		93 %
6	D2O		5 %
7	d-TFE		2 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SIP(189-219)	[U-100% 13C; U-100% 15N]	1 mM
2	S100A6	natural abundance	1 mM
3	TRIS	[U-2H]	0.05 mM
4	Ca2+	natural abundance	0.01 mM
5	H2O		93 %
6	D2O		5 %
7	d-TFE		2 %

6 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SIP(189-219)	[U-100% 13C; U-100% 15N]	1 mM
2	S100A6	natural abundance	1 mM
3	TRIS	[U-2H]	0.05 mM
4	Ca2+	natural abundance	0.01 mM
5	H2O		93 %
6	D2O		5 %
7	d-TFE		2 %

7 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 98% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 13C-labeled SIP(189-219) and unlabeled S100A6. 2% d-TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
15	SIP(189-219)	[U-100% 13C]	1 mM
16	S100A6	natural abundance	1 mM
17	TRIS	[U-2H]	0.05 mM
18	Ca2+	natural abundance	0.01 mM
19	D2O		98 %
20	d-TFE		2 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	SIP(189-219)	[U-100% 13C]	1 mM
16	S100A6	natural abundance	1 mM
17	TRIS	[U-2H]	0.05 mM
18	Ca2+	natural abundance	0.01 mM
19	D2O		98 %
20	d-TFE		2 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
15	SIP(189-219)	[U-100% 13C]	1 mM
16	S100A6	natural abundance	1 mM
17	TRIS	[U-2H]	0.05 mM
18	Ca2+	natural abundance	0.01 mM
19	D2O		98 %
20	d-TFE		2 %

10 3D 13C-filtered 15N-edited NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains 13C-labeled SIP(189-219) and 15N-labeled S100A6. 2% TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
21	SIP(189-219)	[U-100% 13C]	2.3 mM
22	S100A6	[U-100% 15N]	2.3 mM
23	TRIS	[U-2H]	0.05 mM
24	Ca2+	natural abundance	0.01 mM
25	H2O		93 %
26	D2O		5 %
27	d-TFE		2 %

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/5% D2O/2% d-TFE, Pressure 1 atm, Temperature 318 K, pH 6.5, Details Contains unlabeled SIP(189-219) and double-labeled S100A6. 2% TFE was added to improve spectral quality.

#	Name	Isotope labeling	Concentration
28	SIP(189-219)	natural abundance	1 mM
29	S100A6	[U-100% 13C; U-100% 15N]	1 mM
30	TRIS	[U-2H]	0.05 mM
31	Ca2+	natural abundance	0.01 mM
32	H2O		93 %
33	D2O		5 %
34	d-TFE		2 %

12 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
28	SIP(189-219)	natural abundance	1 mM
29	S100A6	[U-100% 13C; U-100% 15N]	1 mM
30	TRIS	[U-2H]	0.05 mM
31	Ca2+	natural abundance	0.01 mM
32	H2O		93 %
33	D2O		5 %
34	d-TFE		2 %

13 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
28	SIP(189-219)	natural abundance	1 mM
29	S100A6	[U-100% 13C; U-100% 15N]	1 mM
30	TRIS	[U-2H]	0.05 mM
31	Ca2+	natural abundance	0.01 mM
32	H2O		93 %
33	D2O		5 %
34	d-TFE		2 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15418_2jtt.nef
Input source #2: Coordindates	2jtt.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	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

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90
MASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90
MASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG

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

---190-------200-------210---------
GPGSSEGLMNVLKKIYEDGDDDMKRTINKAWVESR
|||||||||||||||||||||||||||||||||||
GPGSSEGLMNVLKKIYEDGDDDMKRTINKAWVESR
--------10--------20--------30-----

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

---190-------200-------210---------
GPGSSEGLMNVLKKIYEDGDDDMKRTINKAWVESR
|||||||||||||||||||||||||||||||||||
GPGSSEGLMNVLKKIYEDGDDDMKRTINKAWVESR
--------10--------20--------30-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	90	100.0
B	B	90	100.0
C	C	35	100.0
D	D	35	100.0

Content subtype: combined_15418_2jtt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts	Warning	745		96.7 (chain: A, length: 90), 88.6 (chain: C, length: 35)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	5292 (1)	noe	100.0 (chain: A, length: 90), 100.0 (chain: B, length: 90), 85.7 (chain: C, length: 35), 85.7 (chain: D, length: 35)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	382 (382)	.	83.3 (chain: A, length: 90), 83.3 (chain: B, length: 90), 77.1 (chain: C, length: 35), 77.1 (chain: D, length: 35)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 96.7%
  - Entity_assembly_ID: C, Chain length: 35, Sequence coverage: 88.6%
- Total number of assignments
  - ¹H chemical shifts: 337
  - ¹³C chemical shifts: 295
  - ¹⁵N chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: C
- 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
  - Chain_ID: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	568	147	25.9
¹³C chemical shifts	420	159	37.9
¹⁵N chemical shifts	98	82	83.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	186	104	55.9
¹³C chemical shifts	180	86	47.8
¹⁵N chemical shifts	89	82	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	43	11.3
¹³C chemical shifts	240	73	30.4
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	11	19.0
¹³C chemical shifts	58	6	10.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	0	0.0
¹³C chemical shifts	31	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	212	190	89.6
¹³C chemical shifts	152	136	89.5
¹⁵N chemical shifts	39	31	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	61	83.6
¹³C chemical shifts	70	59	84.3
¹⁵N chemical shifts	34	28	82.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	139	129	92.8
¹³C chemical shifts	82	77	93.9
¹⁵N chemical shifts	5	3	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	9	8	88.9
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 35, Sequence coverage: 85.7%
  - Entity_assembly_ID: D, Chain length: 35, Sequence coverage: 85.7%
- Total number of restraints: 5252
- Weight of restraints: 1.0 (5252)
- Potential type of restraints: upper-bound-parabolic (5252)
- Range of distance target values: 2.0, 6.83 (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
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 83.3%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 83.3%
  - Entity_assembly_ID: C, Chain length: 35, Sequence coverage: 77.1%
  - Entity_assembly_ID: D, Chain length: 35, Sequence coverage: 77.1%
- Total number of restraints: 382
- Total number of restraints per polymer type: 382
- Weight of restraints: 1.0 (382)
- Potential type of restraints: square-well-parabolic (382)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

Keywords beta-catenin, E3 ligase complex, S100A6, Siah-1 interacting protein, ubiquitination

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Found 1 Document (6.419 seconds)

BMRB: 15418

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Related entities 1. S100A6, : 71 entities Detail

Related entities 2. SIP(189-219), : 1 : 9 : 34 entities Detail

Interaction partners 2. SIP(189-219), : 20 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail