BMRBj - BMREntryMaster

Found 1 Document (1.26 seconds)

BMRB: 16671

2KSP

Mechanism for the selective interaction of C-terminal EH-domain proteins with specific NPF-containing partners

Authors

KIEKEN, F., SHARMA, M., JOVIC, M., PANAPAKKAM GIRIDHARAN, S., NASLAVSKY, N., CAPLAN, S., SORGEN, P.

Assembly

EH-domain proteins with specific NPF-containing partners

Entity

1. EH domain of EHD1 (polymer, Thiol state: unknown), 105 monomers, 11635.18 Da Detail

GPLGSDDVEW VVGKDKPTYD EIFYTLSPVN GKITGANAKK EMVKSKLPNT VLGKIWKLAD VDKDGLLDDE EFALANHLIK VKLEGHELPA DLPPHLVPPS KRRHE

2. MICAL L1 like peptide (polymer, Thiol state: unknown), 15 monomers, 1854.872 Da Detail

LESKPYNPFE EEEED

3. CALCIUM ION (non-polymer), 40.078 Da

Total weight

13530.13 Da

Max. entity weight

11635.18 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 81.9 %, Completeness (bb): 73.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.9 % (1161 of 1417)	91.8 % (683 of 744)	69.1 % (385 of 557)	80.2 % (93 of 116)
Backbone	73.5 % (513 of 698)	89.9 % (213 of 237)	60.2 % (212 of 352)	80.7 % (88 of 109)
Sidechain	89.3 % (742 of 831)	92.7 % (470 of 507)	84.2 % (267 of 317)	71.4 % (5 of 7)
Aromatic	86.2 % (81 of 94)	97.9 % (46 of 47)	75.6 % (34 of 45)	50.0 % (1 of 2)
Methyl	95.3 % (122 of 128)	96.9 % (62 of 64)	93.8 % (60 of 64)

1. EH domain of EHD1

GPLGSDDVEW VVGKDKPTYD EIFYTLSPVN GKITGANAKK EMVKSKLPNT VLGKIWKLAD VDKDGLLDDE EFALANHLIK VKLEGHELPA DLPPHLVPPS KRRHE

2. MICAL L1 like peptide

LESKPYNPFE EEEED

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2015-04-08

Citation

Mechanism for the selective interaction of C-terminal Eps15 homology domain proteins with specific Asn-Pro-Phe-containing partners
Kieken, F., Sharma, M., Jovic, M., Giridharan, S., Naslavsky, N., Caplan, S., Sorgen, P.L.
J. Biol. Chem. (2010), 285, 8687-8694, PubMed 20106972 , DOI 10.1074/jbc.M109.045666 , Abstract

Related entities 1. EH domain of EHD1, : 1 : 98 entities Detail

Related entities 2. MICAL L1 like peptide, : 1 : 2 entities Detail

Interaction partners 2. MICAL L1 like peptide, : 23 interactors Detail

More details for 23 interactors identified by 10 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 2D 13CFiltered-13CfilteredNOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 2D 13C-filtered-15N editedNOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 2D 15N filtered Noesy

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Tris, 100Kcl, 2mM Cacl2

#	Name	Isotope labeling	Type	Concentration
1	EH domain of EHD1	[U-99% 13C; U-99% 15N]		0.6 mM
2	MICAL L1 like peptide	natural abundance		2 mM
3	Tris	natural abundance		20 mM
4	Kcl	natural abundance		100 mM
5	Cac12	natural abundance		2 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16671_2ksp.nef
Input source #2: Coordindates	2ksp.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:66:LEU:O	3:1:CA:CA	unknown	unknown	n/a
1:71:GLU:OE2	3:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	CA	CALCIUM ION	None

Sequence alignments

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

----40--------50--------60--------70--------80--------90-------100-------110-------120-------130----
GPLGSDDVEWVVGKDKPTYDEIFYTLSPVNGKITGANAKKEMVKSKLPNTVLGKIWKLADVDKDGLLDDEEFALANHLIKVKLEGHELPADLPPHLVPPS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSDDVEWVVGKDKPTYDEIFYTLSPVNGKITGANAKKEMVKSKLPNTVLGKIWKLADVDKDGLLDDEEFALANHLIKVKLEGHELPADLPPHLVPPS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----
KRRHE
|||||
KRRHE
-----

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

-----150-------
LESKPYNPFEEEEED
|||||||||||||||
LESKPYNPFEEEEED
--------10-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0
B	B	15	0	0	100.0

Content subtype: combined_16671_2ksp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1162		95.2 (chain: A, length: 105), 86.7 (chain: B, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2786 (1)	noe	95.2 (chain: A, length: 105), 86.7 (chain: B, length: 15)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 95.2%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 86.7%
- Total number of assignments
  - ¹H chemical shifts: 705
  - ¹³C chemical shifts: 365
  - ¹⁵N chemical shifts: 92
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 95.2%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 86.7%
- Total number of restraints: 2786
- Weight of restraints: 1.0 (2786)
- Potential type of restraints: square-well-parabolic (2786)
- Range of distance target values: 1.7, 4.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords EHD1