BMRBj - BMREntryMaster

Found 1 Document (1.349 seconds)

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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.349 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail