SASDFN8: Apoferritin from horse spleen - SEC-SAXS coupled to multiangle la...

Basic information

• Entry: Database: SASBDB / ID: SASDFN8

Sample

Apoferritin from horse spleen - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)

• Apoferritin light chain (protein), Equus caballus

Function / homology

Function:

ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / cytoplasm

Domain/homology:

Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily

Component:

Ferritin light chain

• Biological species: Equus caballus (horse)

Contact author

• Melissa Graewert
• Cy M Jeffries

Models

• Model #3208: ; Type: dummy / Software: (SUPCOMB 23 (r9988)) / Radius of dummy atoms: 2.70 A / Symmetry: P1 / Chi-square value: 1.074 / P-value: 0.577890; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3209: ; Type: dummy / Software: (DAMFILT 5.0 (r10552)) / Radius of dummy atoms: 4.00 A / Chi-square value: 1.074 / P-value: 0.577890; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3210: ; Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: P432 / Chi-square value: 5.88; Search similar-shape structures of this assembly by Omokage search (details)
• Model #3212: ; Type: atomic / Software: (PDB) / Chi-square value: 8.846; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Apoferritin from horse spleen - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS); Specimen concentration: 11 mg/ml
• Buffer: Name: 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, / pH: 7 / Comment: Running buffer for SEC-SAXS

Entity #1766

Type: protein / Description: Apoferritin light chain / Formula weight: 19.977 / Num. of mol.: 24 / Source: Equus caballus / References: UniProt: P02791
Sequence:

MSSQIRQNYS TEVEAAVNRL VNLYLRASYT YLSLGFYFDR DDVALEGVCH FFRELAEEKR EGAERLLKMQ NQRGGRALFQ DLQKPSQDEW GTTLDAMKAA IVLEKSLNQA LLDLHALGSA QADPHLCDFL ESHFLDEEVK LIKKMGDHLT NIQRLVGSQA GLGEYLFERL TLKHD

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.123982 Å / Dist. spec. to detc.: 3 mm
• Detector: Name: Pilatus 6M

Scan

Title: Apoferritin from horse spleen - SEC-SAXS coupled to multiangle laser and quasi-elastic light scattering (MALLS and QELS)
Measurement date: Apr 5, 2019 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 85 / Unit: 1/nm /

	Min	Max
Q	0.0923	7.213

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1377 /

	Min	Max
Q	0.0923306	3.89591
P(R) point	1	1377
R	0	12.5

Result

Type of curve: sec
Comments: Apoferritin underwent pre-purification prior SEC-SAXS using the following method. All procedures were performed at 4 oC. An apoferritin stock solution (from equine spleen supplied in ca. 50% v/v glycerol; Sigma Gel Filtration Markers Kit MWGF1000) was diluted two-fold in 25 mM HEPES, 50 mM NaCl, 5 mM urea, 1% v/v glycerol, pH 7. Approximately 200 μl of sample were loaded onto a Superose 6 Increase 10/300 column (GE Healthcare) equilibrated in the same buffer (flow rate = 0.4 ml/min). Fractionated aliquots corresponding to the highest absorbing peak (estimated using UV A280 and UV A245 nm) were pooled and concentrated (30 kDa centrifuge spin filter) to a final concentration of 11 mg/ml (the concentration was determined from triplicate UV A280 measurements using an E0.1% of 0.729 (= 1 g/l) calculated from the amino acid sequence (ProtParam)). Approximately 50 μl aliquots were snap-frozen in liquid nitrogen then stored at -80 oC prior to the SEC-SAXS analysis that was performed at room temperature in 50 mM HEPES, 150 mM NaCl, 2% v/v glycerol, pH 7. The Rg-correlation through the SEC-SAXS peak, the individual unsubtracted SEC-SAXS frames as well as the results from coupled MALLS and QELS analysis are included in the full entry zip archive. The quoted experimental molecular weight was determined using MALLS in combination with refractive-index (RI) measurements that were recorded from the same sample eluting from the column using a split-flow SEC-SAXS-light scattering configuration (Graewert et al., (2015) Sci. Reports. 5, 10734: doi: 10.1038/srep10734). The average hydrodynamic radius of the protein is 6.7 nm.

	Experimental	Porod
MW	454 kDa	424 kDa
Volume	-	679 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	50700	50957.8	21
Radius of gyration, Rg	5.222 nm	5.35 nm	-

	Min	Max
D	-	12.5
Guinier point	1	52