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BMRB: 15016

2JMF

Solution structure of the Su(dx) WW4 - Notch peptide complex

Authors

Avis, J.M., Blankley, R.T., Jennings, M.D., Golovanov, A.P.

Assembly

WW4 - peptide complex

Entity

1. Su(dx) (polymer, Thiol state: not present), 53 monomers, 5921.527 Da Detail

GPLGSPEFHM VSLINEGPLP PGWEIRYTAA GERFFVDHNT RRTTFEDPRP GAP

2. Notch (polymer, Thiol state: not reported), 21 monomers, 2159.375 Da Detail

GPLGSPNTGA KQPPSYEDCI K

Total weight

8080.902 Da

Max. entity weight

5921.527 Da

Source organism

Drosophila melanogaster

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.9 %, Completeness: 87.1 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.1 % (730 of 838)	82.1 % (363 of 442)	92.1 % (303 of 329)	95.5 % (64 of 67)
Backbone	90.5 % (380 of 420)	89.7 % (130 of 145)	89.7 % (191 of 213)	95.2 % (59 of 62)
Sidechain	85.1 % (411 of 483)	78.5 % (233 of 297)	95.6 % (173 of 181)	100.0 % (5 of 5)
Aromatic	89.5 % (68 of 76)	78.9 % (30 of 38)	100.0 % (37 of 37)	100.0 % (1 of 1)
Methyl	92.6 % (50 of 54)	92.6 % (25 of 27)	92.6 % (25 of 27)

1. Su(dx)

GPLGSPEFHM VSLINEGPLP PGWEIRYTAA GERFFVDHNT RRTTFEDPRP GAP

2. Notch

GPLGSPNTGA KQPPSYEDCI K

Show sample condition

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2JMF, Strand ID: A, B Detail

Release date

2007-10-08

Citation

Specificity and autoregulation of Notch binding by tandem WW domains in suppressor of Deltex
Jennings, M.D., Blankley, R.T., Baron, M., Golovanov, A.P., Avis, J.M.
J. Biol. Chem. (2007), 282, 29032-29042, PubMed 17656366 , DOI 10.1074/jbc.M703453200 , Abstract

Related entities 1. Su(dx), : 2 : 26 entities Detail

Related entities 2. Notch, : 1 : 4 entities Detail

Interaction partners 1. Su(dx), : 9 interactors Detail

More details for 9 interactors identified by 3 citations

Interaction partners 2. Notch, : 14 interactors Detail

More details for 14 interactors identified by 9 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

2 2D 1H-15N HSQC

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

3 3D HNCO

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

4 3D HNCO

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

5 3D HNCA

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

6 3D HNCA

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

7 3D HNCACB

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

8 3D HNCACB

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

9 3D HN(CO)CA

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

10 3D HN(CO)CA

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

11 3D HCCH-TOCSY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

12 3D HCCH-TOCSY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

13 3D 1H-15N NOESY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

14 3D 1H-15N NOESY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

15 3D 1H-15N TOCSY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

16 3D 1H-15N TOCSY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

17 3D 1H-13C NOESY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

18 3D 1H-13C NOESY

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

19 2D 1H-13C HSQC

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
1	Su(dx)	[U-13C; U-15N]		0.4 ~ 0.6 mM
2	Notch	natural abundance		1.5 ~ 2.5 mM
3	sodium chloride			45 mM
4	DTT			9 mM
5	EDTA			0.9 mM
6	Arginine			45 mM
7	Glutamate			45 mM
8	D2O			10 %

20 2D 1H-13C HSQC

Instrument

Bruker AMX - 600 MHz Fitted with a Cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 293 K, pH 6.75

#	Name	Isotope labeling	Type	Concentration
9	Notch	[U-13C; U-15N]		0.4 ~ 0.6 mM
10	Su(dx)	natural abundance		1.5 ~ 2.5 mM
11	sodium chloride			45 mM
12	DTT			9 mM
13	EDTA			0.9 mM
14	Arginine			45 mM
15	Glutamate			45 mM
16	D2O			10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15016_2jmf.nef
Input source #2: Coordindates	2jmf.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

---510-------520-------530-------540-------550-------
GPLGSPEFHMVSLINEGPLPPGWEIRYTAAGERFFVDHNTRRTTFEDPRPGAP
|||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSPEFHMVSLINEGPLPPGWEIRYTAAGERFFVDHNTRRTTFEDPRPGAP
--------10--------20--------30--------40--------50---

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

----2320------2330---
GPLGSPNTGAKQPPSYEDCIK
|||||||||||||||||||||
GPLGSPNTGAKQPPSYEDCIK
--------10--------20-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0
B	B	21	0	0	100.0

Content subtype: combined_15016_2jmf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	730		90.6 (chain: A, length: 53), 100.0 (chain: B, length: 21)
1	Distance restraints	DYANA/DIANA_distance_constraints_8	Warning	141 (1)	noe	71.7 (chain: A, length: 53), 38.1 (chain: B, length: 21)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	18 (1)	hbond	15.1 (chain: A, length: 53), 9.5 (chain: B, length: 21)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	18 (1)	hbond	15.1 (chain: A, length: 53), 9.5 (chain: B, length: 21)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	54 (54)	.	60.4 (chain: A, length: 53), 47.6 (chain: B, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 90.6%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 362
  - ¹³C chemical shifts: 305
  - ¹⁵N chemical shifts: 63
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- 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: B

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_8
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 71.7%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 38.1%
- Total number of restraints: 141
- Weight of restraints: 1.0 (141)
- Potential type of restraints: upper-bound-parabolic (141)
- Range of distance target values: 4.0, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 15.1%
    - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 9.5%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: upper-bound-parabolic (18)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 15.1%
      - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 9.5%
    - Total number of restraints: 18
    - Weight of restraints: 1.0 (18)
    - Potential type of restraints: lower-bound-parabolic (18)
    - Range of distance target values: 1.8, 2.7 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 60.4%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 47.6%
- Total number of restraints: 54
- Total number of restraints per polymer type: 54
- Weight of restraints: 1.0 (54)
- Potential type of restraints: square-well-parabolic (54)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords complex, Notch, WW domain, NMR solution