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BMRB: 16970

2KYM

Solution structure of the Bem1p SH3-CI domain from L.elongisporus in complex with Ste20p peptide

Authors

Gorelik, M., Muhandiram, R., Davidson, A.R.

Assembly

Bem1p SH3-CI domain with Ste20p

Entity

1. Bud emergence protein 1 (polymer, Thiol state: all free), 120 monomers, 13757.37 Da Detail

MAPLFAVTLY EFKAERDDEL DVSPGENLSI CAHYDYEWFI AKPINRLGGP GLVPVSYVRI IDLMDPAKYA SVDTYDREQV MKIIDEFKIP TVEQWKDQTR RYKESSIQIG NGHGQSQGLE

2. Peptide from Serine/Threonine kinase Ste20 (polymer, Thiol state: not present), 16 monomers, 1636.890 Da Detail

GKFIPSRPAP KPPSSA

Total weight

15394.26 Da

Max. entity weight

13757.37 Da

Source organism

Lodderomyces elongisporus , Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.8 %, Completeness (bb): 91.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.8 % (1461 of 1609)	93.8 % (792 of 844)	87.3 % (550 of 630)	88.1 % (119 of 135)
Backbone	91.0 % (721 of 792)	95.9 % (258 of 269)	88.0 % (351 of 399)	90.3 % (112 of 124)
Sidechain	89.8 % (848 of 944)	92.5 % (532 of 575)	86.6 % (310 of 358)	54.5 % (6 of 11)
Aromatic	87.7 % (121 of 138)	91.3 % (63 of 69)	83.6 % (56 of 67)	100.0 % (2 of 2)
Methyl	94.0 % (126 of 134)	94.0 % (63 of 67)	94.0 % (63 of 67)

1. Bud emergence protein 1

MAPLFAVTLY EFKAERDDEL DVSPGENLSI CAHYDYEWFI AKPINRLGGP GLVPVSYVRI IDLMDPAKYA SVDTYDREQV MKIIDEFKIP TVEQWKDQTR RYKESSIQIG NGHGQSQGLE

2. Peptide from Serine/Threonine kinase Ste20

GKFIPSRPAP KPPSSA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
20	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
21	Ste20 peptide	natural abundance	0.5 mM
22	sodium chloride	natural abundance	100 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium azide	natural abundance	0.05 %
25	H2O	natural abundance	95 %
26	D2O	natural abundance	5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
27	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
28	Ste20 peptide	natural abundance	0.5 mM
29	sodium chloride	natural abundance	100 mM
30	sodium phosphate	natural abundance	50 mM
31	sodium azide	natural abundance	0.05 %
32	D2O	natural abundance	100 %

Protein Blocks Logo

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

Release date

2010-06-30

Citation

A Conserved residue in the yeast Bem1p SH3 domain maintains the high level of binding specificity required for function
Gorelik, M., Stanger, K., Davidson, A.R.
J. Biol. Chem. (2011), 286, 19470-19477, PubMed 21489982 , DOI 10.1074/jbc.M111.229294 , Abstract

Related entities 1. Bud emergence protein 1, : 7 entities Detail

Related entities 2. Peptide from Serine/Threonine kinase Ste20, : 1 : 4 : 6 entities Detail

Interaction partners 2. Peptide from Serine/Threonine kinase Ste20, : 35 : 1 interactors Detail

More details for 36 interactors identified by 16 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

2 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

3 3D HN(CO)CA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

4 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

6 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

7 3D HNCA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
2	Ste20 peptide	natural abundance	1.5 (±0.1) mM
3	PMSF	natural abundance	0.5 mM
4	EDTA	natural abundance	0.5 mM
5	sodium azide	natural abundance	0.05 %
6	HEPES	natural abundance	50 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	1 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

8 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

10 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

12 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
11	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.7 (±0.05) mM
12	Ste20 peptide	natural abundance	1.5 (±0.1) mM
13	PMSF	natural abundance	0.5 mM
14	EDTA	natural abundance	0.5 mM
15	sodium azide	natural abundance	0.05 %
16	HEPES	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	D2O	natural abundance	100 %

13 15N C13 filtered 2D 1H-1H TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
20	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
21	Ste20 peptide	natural abundance	0.5 mM
22	sodium chloride	natural abundance	100 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium azide	natural abundance	0.05 %
25	H2O	natural abundance	95 %
26	D2O	natural abundance	5 %

14 15N C13 filtered 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
20	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
21	Ste20 peptide	natural abundance	0.5 mM
22	sodium chloride	natural abundance	100 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium azide	natural abundance	0.05 %
25	H2O	natural abundance	95 %
26	D2O	natural abundance	5 %

15 15N C13 filtered 2D 1H-1H COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
27	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
28	Ste20 peptide	natural abundance	0.5 mM
29	sodium chloride	natural abundance	100 mM
30	sodium phosphate	natural abundance	50 mM
31	sodium azide	natural abundance	0.05 %
32	D2O	natural abundance	100 %

16 13C half-filtered 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
27	Bem1 SH3-CI protein	[U-99% 13C; U-99% 15N]	0.5 (±0.05) mM
28	Ste20 peptide	natural abundance	0.5 mM
29	sodium chloride	natural abundance	100 mM
30	sodium phosphate	natural abundance	50 mM
31	sodium azide	natural abundance	0.05 %
32	D2O	natural abundance	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16970_2kym.nef
Input source #2: Coordindates	2kym.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	28	.	Not matched with CCD	None
A	29	.	Not matched with CCD	None
A	31	.	Not matched with CCD	None
A	33	.	Not matched with CCD	None
A	34	.	Not matched with CCD	None
A	35	.	Not matched with CCD	None
A	39	.	Not matched with CCD	None
A	41	.	Not matched with CCD	None
A	42	.	Not matched with CCD	None
A	43	.	Not matched with CCD	None
A	44	.	Not matched with CCD	None
A	45	.	Not matched with CCD	None
A	46	.	Not matched with CCD	None
A	47	.	Not matched with CCD	None
A	48	.	Not matched with CCD	None
A	49	.	Not matched with CCD	None
A	51	.	Not matched with CCD	None
A	52	.	Not matched with CCD	None
A	53	.	Not matched with CCD	None
A	54	.	Not matched with CCD	None
A	55	.	Not matched with CCD	None
A	57	.	Not matched with CCD	None
A	58	.	Not matched with CCD	None
A	59	.	Not matched with CCD	None
A	60	.	Not matched with CCD	None
A	61	.	Not matched with CCD	None
A	62	.	Not matched with CCD	None
A	63	.	Not matched with CCD	None
A	64	.	Not matched with CCD	None
A	65	.	Not matched with CCD	None
A	66	.	Not matched with CCD	None
A	67	.	Not matched with CCD	None
A	68	.	Not matched with CCD	None
A	69	.	Not matched with CCD	None
A	70	.	Not matched with CCD	None
A	71	.	Not matched with CCD	None
A	72	.	Not matched with CCD	None
A	73	.	Not matched with CCD	None
A	74	.	Not matched with CCD	None
A	83	.	Not matched with CCD	None
A	84	.	Not matched with CCD	None
A	85	.	Not matched with CCD	None
A	86	.	Not matched with CCD	None
A	87	.	Not matched with CCD	None
A	88	.	Not matched with CCD	None
A	89	.	Not matched with CCD	None

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	120	87	2	24.2

Content subtype: combined_16970_2kym.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1480		No information
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Error	3644 (1)	noe	No information
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	81 (1)	hbond	40.3 (chain: A, length: 77)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	Warning	144 (144)	.	1.3 (chain: A, length: 77)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Error
- Experiment type: noe
- Total number of restraints: 3644
- Weight of restraints: 1.0 (3644)
- Potential type of restraints: upper-bound-parabolic (3644)
- Range of distance target values: 2.29, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 40.3%
  - Total number of restraints: 81
  - Weight of restraints: 1.0 (81)
  - Potential type of restraints: upper-bound-parabolic (81)
  - Range of distance target values: 1.8, 3.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 1.3%
- Total number of restraints: 144
- Total number of restraints per polymer type: 144
- Weight of restraints: 1.0 (144)
- Potential type of restraints: square-well-parabolic (144)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords Bem1p, Cdc42p-interacting, scaffold, SH3-CI, SH3 domain, Ste20p PRR

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Found 1 Document (1.427 seconds)

BMRB: 16970

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Bud emergence protein 1, : 7 entities Detail

Related entities 2. Peptide from Serine/Threonine kinase Ste20, : 1 : 4 : 6 entities Detail

Interaction partners 2. Peptide from Serine/Threonine kinase Ste20, : 35 : 1 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail