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BMRB: 19447

2MCN

DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: MOLECULAR DETERMINANTS AND FUNCTIONAL IMPLICATIONS

Authors

Ortega-Roldan, J., Salmon, L., Azuaga, A., Blackledge, M., Van Nuland, N.

Assembly

Ubiquitin Binding with SH3 domains

Entity

1. SH3A (polymer, Thiol state: not present), 61 monomers, 7271.007 Da Detail

VDYIVEYDYD AVHDDELTIR VGEIIRNVKK LQEEGWLEGE LNGRRGMFPD NFVKEIKRET E

2. Ubiquitin (polymer, Thiol state: not present), 76 monomers, 8564.731 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Total weight

15835.738 Da

Max. entity weight

8564.731 Da

Source organism

Mus musculus , Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics, docking, simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 46.0 %, Completeness: 13.7 %, Completeness (bb): 30.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	13.7 % (138 of 1010)	8.8 % (76 of 864)	42.5 % (62 of 146)
Backbone	30.7 % (127 of 414)	23.1 % (65 of 281)	46.6 % (62 of 133)
Sidechain	1.8 % (11 of 596)	1.9 % (11 of 583)	0.0 % (0 of 13)
Aromatic	0.0 % (0 of 47)	0.0 % (0 of 46)	0.0 % (0 of 1)
Methyl	1.2 % (1 of 82)	1.2 % (1 of 82)

1. SH3A

VDYIVEYDYD AVHDDELTIR VGEIIRNVKK LQEEGWLEGE LNGRRGMFPD NFVKEIKRET E

2. Ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.2 mM [U-99% 15N] CD2AP SH3-A, 1 mM UBIQUITIN, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CD2AP SH3-A	[U-99% 15N]	0.2 mM
2	Ubiquitin	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.25 mM [U-99% 15N] UBIQUITIN, mM CD2AP SH3-A, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	CD2AP SH3-A	natural abundance	0.0 ~ 0.0 mM
6	Ubiquitin	[U-99% 15N]	0.25 mM
7	H2O	natural abundance	90 %
8	D2O	[U-100% 2H]	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.9 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 0.46 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
9	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.9 mM
10	Ubiquitin	[U-99% 15N]	0.46 mM
11	H2O	natural abundance	90 %
12	D2O	[U-100% 2H]	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.8 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.37 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
13	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.8 mM
14	Ubiquitin	[U-99% 15N]	1.37 mM
15	H2O	natural abundance	90 %
16	D2O	[U-100% 2H]	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.7 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.75 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
17	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.7 mM
18	Ubiquitin	[U-99% 15N]	1.75 mM
19	H2O	natural abundance	90 %
20	D2O	[U-100% 2H]	10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-A, 1.75 MM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
21	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.25 mM
22	Ubiquitin	[U-99% 15N]	1.75 mM
23	H2O	natural abundance	90 %
24	D2O	[U-100% 2H]	10 %

Chem. Shift Complete2

Sequence coverage: 52.6 %, Completeness: 15.0 %, Completeness (bb): 33.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	15.0 % (302 of 2020)	9.7 % (168 of 1728)	45.9 % (134 of 292)
Backbone	33.1 % (274 of 828)	24.9 % (140 of 562)	50.4 % (134 of 266)
Sidechain	2.3 % (28 of 1192)	2.4 % (28 of 1166)	0.0 % (0 of 26)
Aromatic	0.0 % (0 of 94)	0.0 % (0 of 92)	0.0 % (0 of 2)
Methyl	1.8 % (3 of 164)	1.8 % (3 of 164)

1. SH3A

VDYIVEYDYD AVHDDELTIR VGEIIRNVKK LQEEGWLEGE LNGRRGMFPD NFVKEIKRET E

2. Ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.2 mM [U-99% 15N] CD2AP SH3-A, 1 mM UBIQUITIN, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CD2AP SH3-A	[U-99% 15N]	0.2 mM
2	Ubiquitin	natural abundance	1 mM
3	H2O	natural abundance	90 %
4	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.25 mM [U-99% 15N] UBIQUITIN, mM CD2AP SH3-A, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	CD2AP SH3-A	natural abundance	0.0 ~ 0.0 mM
6	Ubiquitin	[U-99% 15N]	0.25 mM
7	H2O	natural abundance	90 %
8	D2O	[U-100% 2H]	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.9 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 0.46 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
9	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.9 mM
10	Ubiquitin	[U-99% 15N]	0.46 mM
11	H2O	natural abundance	90 %
12	D2O	[U-100% 2H]	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.8 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.37 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
13	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.8 mM
14	Ubiquitin	[U-99% 15N]	1.37 mM
15	H2O	natural abundance	90 %
16	D2O	[U-100% 2H]	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.7 mM [U-99% 13CU-99% 15N] CD2AP SH3-A, 1.75 mM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
17	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.7 mM
18	Ubiquitin	[U-99% 15N]	1.75 mM
19	H2O	natural abundance	90 %
20	D2O	[U-100% 2H]	10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-A, 1.75 MM [U-99% 15N] UBIQUITIN,

#	Name	Isotope labeling	Concentration
21	CD2AP SH3-A	[U-99% 13C; U-99% 15N]	0.25 mM
22	Ubiquitin	[U-99% 15N]	1.75 mM
23	H2O	natural abundance	90 %
24	D2O	[U-100% 2H]	10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MCN, Strand ID: A, B Detail

Release date

2014-02-02

Citation

Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications
Ortega-Roldan, J., Casares, S., Ringkjobing-Jensen, M., Cardenes, N., Bravo, N., Blackledge, M., Azuaga, A., Van Nuland, N.
PLoS One (2013), 8, e73018-e73018, PubMed 24039852 , DOI 10.1371/journal.pone.0073018 , Abstract

Related entities 1. SH3A, : 1 : 10 : 2 : 349 entities Detail

Related entities 2. Ubiquitin, : 92 : 6 : 47 : 182 entities Detail

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details 0.25 mM [U-99% 15N] UBIQUITIN, mM CD2AP SH3-A, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	CD2AP SH3-A	natural abundance	0.0 ~ 0.0 mM
6	Ubiquitin	[U-99% 15N]	0.25 mM
7	H2O	natural abundance	90 %
8	D2O	[U-100% 2H]	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_19447_2mcn.nef
Input source #2: Coordindates	2mcn.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

None

Sequence alignments

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

-------10--------20--------30--------40--------50--------60--
VDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETE
--------10--------20--------30--------40--------50--------60-

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

--------10--------20--------30--------40--------50--------60--------70------
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0
B	B	76	0	0	100.0

Content subtype: combined_19447_2mcn.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	CD2AP_SH3-A	Warning	120		98.4 (chain: A, length: 61)
2	Assigned chemical shifts	Ubiquitin-CS	Warning	144		94.7 (chain: B, length: 76)

Assigned chemical shifts

Saveframe: CD2AP_SH3-A
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 60
  - ¹⁵N chemical shifts: 60
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: Ubiquitin-CS
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 76, Sequence coverage: 94.7%
- Total number of assignments
  - ¹H chemical shifts: 72
  - ¹⁵N chemical shifts: 72
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	386	59	15.3
¹⁵N chemical shifts	70	60	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	59	46.8
¹⁵N chemical shifts	60	60	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	260	0	0.0
¹⁵N chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	478	72	15.1
¹⁵N chemical shifts	85	72	84.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	72	46.5
¹⁵N chemical shifts	73	72	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	0	0.0

Keywords SIGNALING PROTEIN

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Found 1 Document (4.855 seconds)

BMRB: 19447

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Sample #6

Related entities 1. SH3A, : 1 : 10 : 2 : 349 entities Detail

Related entities 2. Ubiquitin, : 92 : 6 : 47 : 182 entities Detail

Interaction partners 1. SH3A, : 18 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 3 contents Detail