SASDAP5: Native complex CytC_Adr (Cytochrome C dimer, Cyt_C_dimer + Adreno...

Basic information

• Entry: Database: SASBDB / ID: SASDAP5

Sample

Native complex CytC_Adr

• Cytochrome C dimer (protein), Cyt_C_dimer, Escherichia coli
• Adrenodoxin dimer (protein), Adrenodoxin dimer, Escherichia coli

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: J Am Chem Soc / Year: 2008; Title: Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy.; Authors: Xingfu Xu / Wolfgang Reinle / Frank Hannemann / Peter V Konarev / Dmitri I Svergun / Rita Bernhardt / Marcellus Ubbink / ; Abstract: In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex.

Contact author

• Petr Konarev (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #133: ; Type: dummy / Software: Dammin / Radius of dummy atoms: 1.90 A / Chi-square value: 24.000201; Search similar-shape structures of this assembly by Omokage search (details)
• Model #134: ; Type: mix / Software: Sasref / Radius of dummy atoms: 1.90 A / Chi-square value: 3.8809; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Native complex CytC_Adr / Sample MW: 44 kDa / Specimen concentration: 2.40-24.00 / Entity id: 110 / 111
• Buffer: Name: HEPES / Concentration: 20.00 mM / pH: 7.4 / Composition: DTT 2.000 mM

Entity #110

Name: Cyt_C_dimer / Type: protein / Description: Cytochrome C dimer / Formula weight: 11 / Num. of mol.: 2 / Source: Escherichia coli
Sequence:

TEFKAGSAKK GATLFKTRCL QCHTVEKGGP HKVGPNLHGI FGRHSGQAEG YSYTDANIKK NVLWDENNMS EYLTNPKKYI PGTKMAFGGL KKEKDRNDLI TYLKKATE

Entity #111

Name: Adrenodoxin dimer / Type: protein / Description: Adrenodoxin dimer / Formula weight: 11 / Num. of mol.: 2 / Source: Escherichia coli
Sequence:

KITVHFINRD GETLTTKGKI GDSLLDVVVQ NNLDIDGFGA CEGTLACSTC HLIFEQHIFE KLEEAITDEE NDMLDLAYGL TDDRSRLGCQ ICLTKAMDNM TVRVP

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron
• Detector: Name: MAR 345 Image Plate

Scan

Title: Native complex (Cyt_C_Adr) / Measurement date: Jun 15, 2006 / Storage temperature: 15 °C / Cell temperature: 15 °C / Exposure time: 120 sec. / Number of frames: 2 / Unit: 1/nm /

	Min	Max
Q	0.2004	4.9853

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 512 /

	Min	Max
Q	0.2038	4.848
P(R) point	1	512
R	0	9.5

Result

D max: 9.5 / Type of curve: merged /

	Experimental	Standard	Porod
MW	44 kDa	42 kDa	44 kDa
Volume	-	-	64 nm3

	P(R)	Guinier
Forward scattering, I0	11.5	11.3
Radius of gyration, Rg	3 nm	2.9 nm