PICK1 LKV Decomposed Dimer:

The addtional folders contain:
- "Original_SAXS_data_POR" folder with original background subtracted data scaled to 1 mg/ml using BSA as standard (BSA SAXS data included). The data consist of a concentration series of PICK1 LKV, and corresponding Gnom output files.
- "Rescaled_Data" folder containing the same data and Gnom output files on absolute scale [cm^-1/(mg/ml)] and a slight rescaling to ensure overlap of concentration-insensitive region of scattering curve. RebinnedRescaled subfolder contains data rebinned to logarithmically equidistant points. 
- "Decomposed_FF_Dimer_EOM" contains a decomposed "form factor" derived from a combination of the scattering of two samples, using a novel approach developed in Karlsen et.al. 2015. Both a rebinned (prefix: R) and non-rebinned data file are included. It furthermore contains the result of an EOM analysis on the rebinned data yielding the included ensemble of structures.


-------------------
Database entry fields are as follows:

Title:
PICK1 LKV, Dimer from decomposition of data from polydisperse samples.

Contributor:
Morten L. Karlsen,
Thor S. Thorsen, Niklaus Johner, Ina Ammendrup-Johnsen, Simon Erlendsson, Xinsheng Tian, Jens B. Simonsen, Rasmus Høiberg-Nielsen, Nikolaj M. Christensen, George Khelashvili, Werner Streicher, Kaare Teilum, Bente Vestergaard, Harel Weinstein, Ulrik Gether, Lise Arleth and Kenneth L. Madsen.

Email:

Short description:
Structure and flexibility of PICK1 LKV mutant dimer was characterized by SAXS, using data obtained by decomposing scattering from two polydisperse samples into dimer (and tetramer) contributions. To obtain the dimer scattering, two samples were measured at 4.4 and 8,8 mg/ml, and decomposed as described in the reference. Models were fitted to data using a combination of rigid body modelling and EOM, based on structural components defined by NMR and MD simulations. PDB files represent structures found in the optimal ensemble.

Reference:
Morten L. Karlsen, Thor S. Thorsen, Niklaus Johner, Ina Ammendrup-Johnsen, Simon Erlendsson, Xinsheng Tian, Jens B. Simonsen, Rasmus Høiberg-Nielsen, Nikolaj M. Christensen, George Khelashvili, Werner Streicher, Kaare Teilum, Bente Vestergaard, Harel Weinstein, Ulrik Gether, Lise Arleth and Kenneth L. Madsen.
Structure of dimeric and tetrameric complexes of the BAR domain protein PICK1 determined by small-angle X-ray scattering.
Structure, Accepted, Publication Pending


Molecule:
PICK1 (Protein Interacting with C-Kinase 1), 3 C-terminal residues substituted with LKV.

Type: 
Protein

Fragment:
Full Length (1-416)

FASTA:
MFADLDYDIEEDKLGIPTVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAAL
DGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQADPKQGMSLDIVLKK
VKHRLVENMSSGTADALGLSRAILCNDGLVKRLEELERTAELYKGMTEHTKNLLRAFYEL
SQTHRAFGDVFSVIGVREPQPAASEAFVKFADAHRSIEKFGIRLLKTIKPMLTDLNTYLN
KAIPDTRLTIKKYLDVKFEYLSYCLKVKEMDDEEYSCIALGEPLYRVSTGNYEYRLILRC
RQEARARFSQMRKDVLEKMELLDQKHVQDIVFQLQRLVSTMSKYYNDCYAVLRDADVFPI
EVDLAHTTLAYGPNQGGFTDGEDEEEEEEDGAAREVSKDARGATGPTDKGGSWLKV

Organism:
Rattus norvegicus

Uniprot ID:
Q9EP80

Oligomeric State:
Dimer / Tetramer

Monomer Mol. Weight:
46.61 kD


EXPERIMENTAL DETAILS:
EXPERIMENT DESCRIPTION:
X-ray synchrotron radiation scattering data from solutions of PICK1 in 50 mM Tris, pH 7.4, 125 mM NaCl and 0.01 vol% reduced TX-100  were collected on the X33 camera on the storage ring DORIS (Hamburg, Germany). Using a MAR345 image plate, the range of momentum transfer  0.008 < q < 0.496 Å^{-1} was covered (s = 4π sin θ/λ, where 2θ is the scattering angle). Different solute concentrations in the range 1.5-8.8 mg/ml were measured. Four successive 30 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The dimeric and tetrameric components of the data were extracted by decomposition of two samples at different concentrations, as described in the reference.

Date:
May 2010

Type:
Synchrotron

Beamline:
X33,EMBL/DESY, Hamburg, Germany

X-ray wavelength:

Number of Frames:
4

Exp. pr. frame:
30

Detector:
MAR345 image plate

Temperature
4

Sample-detector distance:
2.7m

Type:
Merged (Actually it is "Decomposed" from two concentrations both containing two oligomeric states)

Min. Concentration:
4.2

Max Concentration:
8.8

Buffer:
50 mM Tris, pH 7.4, 125 mM NaCl and 0.01 vol% reduced TX-100

Data File:
RX36vs38.dat

P(r) file:
fiti.dat

OVERALL PARAMETERS:
I(0) Guinier:
N/A

R_g Guinier:
N/A

MW Guinier:
92

MW from Porod:
N/A

I(0) p(r):
1.033

Rg p(r):
6.097 1/nm

Dmax:
20.0

Porod Volume:
N/A

