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BMRB: 16179

2KFF

Structure of the C-terminal domain of EHD1 with FNYESTNPFTAK

Authors

KIEKEN, F., JOVIC, M., TONELLI, M., NASLAVSKY, N., CAPLAN, S., SORGEN, P.

Assembly

EHD1 with FNYESTNPFTAK

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. Rab11-FIP2 NPF peptide (polymer, Thiol state: unknown), 12 monomers, 1418.505 Da Detail

FNYESTNPFT AK

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

Total weight

13093.763 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: 94.9 %, Completeness: 81.5 %, Completeness (bb): 72.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.5 % (1126 of 1382)	91.4 % (660 of 722)	68.8 % (375 of 545)	79.1 % (91 of 115)
Backbone	72.4 % (494 of 682)	88.8 % (206 of 232)	58.9 % (202 of 343)	80.4 % (86 of 107)
Sidechain	89.6 % (725 of 809)	92.7 % (454 of 490)	85.5 % (266 of 311)	62.5 % (5 of 8)
Aromatic	76.9 % (80 of 104)	86.5 % (45 of 52)	68.0 % (34 of 50)	50.0 % (1 of 2)
Methyl	94.6 % (123 of 130)	96.9 % (63 of 65)	92.3 % (60 of 65)

1. EH domain of EHD1

GPLGSDDVEW VVGKDKPTYD EIFYTLSPVN GKITGANAKK EMVKSKLPNT VLGKIWKLAD VDKDGLLDDE EFALANHLIK VKLEGHELPA DLPPHLVPPS KRRHE

2. Rab11-FIP2 NPF peptide

FNYESTNPFT AK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

Protein Blocks Logo

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

Release date

2015-04-08

Citation

Structural insight into the interaction of proteins containing NPF, DPF, and GPF motifs with the C-terminal EH-domain of EHD1
Kieken, F., Jovic, M., Tonelli, M., Naslavsky, N., Caplan, S., Sorgen, P.L.
Protein Sci. (2009), 18, 2471-2479, PubMed 19798736 , DOI 10.1002/pro.258 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 16180 released on 2015-04-08
    Title Structure of the C-terminal domain of EHD1 in complex with FNYESTNPFTAK
  BMRB: 16181 released on 2015-04-08
    Title Structure of the C-terminal domain of EHD1 with FNYESTGPFTAK

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

Related entities 2. Rab11-FIP2 NPF peptide, : 1 : 3 : 4 entities Detail

Interaction partners 2. Rab11-FIP2 NPF peptide, : 27 interactors Detail

More details for 27 interactors identified by 7 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

3 3D HNCACB

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

5 3D 1H-13C NOESY

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

6 2D 13CFiltered-13CfilteredNOESY

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

7 2D 13C-filtered-13C editedNOESY

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

8 2D 13C-filtered-15N editedNOESY

Instrument

Varian VXRS - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

9 2D 15N filtered Noesy

Instrument

Varian INOVA - 600 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 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	Rab11-FIP2 NPF peptide	natural abundance		3 mM
3	H20	natural abundance		90 %
4	D20	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16179_2kff.nef
Input source #2: Coordindates	2kff.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	Error

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----
FNYESTNPFTAK
||||||||||||
FNYESTNPFTAK
--------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	12	0	0	100.0

Content subtype: combined_16179_2kff.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	Error	1109		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3319 (1)	noe	95.2 (chain: A, length: 105), 83.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

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: 12, Sequence coverage: 83.3%
- Total number of restraints: 3319
- Weight of restraints: 1.0 (3319)
- Potential type of restraints: square-well-parabolic (3319)
- Range of distance target values: 1.65, 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