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BMRB: 16180

2KFG

Structure of the C-terminal domain of EHD1 in complex with FNYESTNPFTAK

Authors

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

Assembly

EHD1/FNYESTNPFTAK complex

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 DPF peptide (polymer, Thiol state: unknown), 12 monomers, 1419.490 Da Detail

FNYESTDPFT AK

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

Total weight

13094.748 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: 81.9 %, Completeness (bb): 73.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.9 % (1130 of 1379)	92.5 % (666 of 720)	68.4 % (373 of 545)	79.8 % (91 of 114)
Backbone	73.0 % (498 of 682)	90.5 % (210 of 232)	58.9 % (202 of 343)	80.4 % (86 of 107)
Sidechain	89.8 % (724 of 806)	93.4 % (456 of 488)	84.6 % (263 of 311)	71.4 % (5 of 7)
Aromatic	78.8 % (82 of 104)	90.4 % (47 of 52)	68.0 % (34 of 50)	50.0 % (1 of 2)
Methyl	91.5 % (119 of 130)	93.8 % (61 of 65)	89.2 % (58 of 65)

1. EH domain of EHD1

GPLGSDDVEW VVGKDKPTYD EIFYTLSPVN GKITGANAKK EMVKSKLPNT VLGKIWKLAD VDKDGLLDDE EFALANHLIK VKLEGHELPA DLPPHLVPPS KRRHE

2. Rab11-FIP2 DPF peptide

FNYESTDPFT 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: 2KFG, 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

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

Related entities 2. Rab11-FIP2 DPF peptide, : 1 : 2 : 1 : 2 entities Detail

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_16180_2kfg.nef
Input source #2: Coordindates	2kfg.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
1:71:GLU:OE1	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----
FNYESTDPFTAK
||||||||||||
FNYESTDPFTAK
--------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_16180_2kfg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1153		94.3 (chain: A, length: 105), 100.0 (chain: B, length: 12)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3099 (1)	noe	94.3 (chain: A, length: 105), 100.0 (chain: B, length: 12)

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: 94.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 697
  - ¹³C chemical shifts: 365
  - ¹⁵N chemical shifts: 91
- 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: 94.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 3099
- Weight of restraints: 1.0 (3099)
- Potential type of restraints: square-well-parabolic (3099)
- Range of distance target values: 1.75, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords EHD1