SASDFR4: HP2042 form from Helicobacter pylori, N-terminal domain of syntax...

Basic information

• Entry: Database: SASBDB / ID: SASDFR4

Sample

HP2042 form from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, Trp repressor from Escherichia coli (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:1WRT))

• HP2042 form from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, Trp repressor from Escherichia coli (protein), Fusion protein1, Helicobacter pylori, Rattus norvegicus, Escherichia coli

• Biological species: Helicobacter pylori (bacteria); Rattus norvegicus (Norway rat); Escherichia coli (E. coli)
• Citation: Journal: ACS Synth Biol / Year: 2019; Title: Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.; Authors: Takaaki Miyamoto / Yugo Hayashi / Keito Yoshida / Hiroki Watanabe / Takayuki Uchihashi / Kento Yonezawa / Nobutaka Shimizu / Hironari Kamikubo / Shun Hirota / ; Abstract: Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. According to ab initio structural models reconstructed from the small-angle X-ray scattering data, the tetramer of 1 and hexamer of 2 adopted quadrangle and cage-like structures, respectively, although they were combinations of different conformations. High-speed atomic force microscopy observations indicated that the tetramer and hexamer exhibit conformational dynamics. These results show that the present method utilizing three-helix bundle-linked fusion proteins is useful in the construction of protein nanostructures.

Contact author

• Hironari Kamikubo (Nara Institute of Science and Technology)

Models

• Model #2929: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.10 / P-value: 0.046149; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: HP2042 form from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, Trp repressor from Escherichia coli (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:1WRT)); Specimen concentration: 2.30-8.30
• Buffer: Name: 20 mM Tris-HCl 150 mM NaCl / pH: 8

Entity #1582

Name: Fusion protein1 / Type: protein
Description: HP2042 form from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, Trp repressor from Escherichia coli
Formula weight: 37.434 / Num. of mol.: 4
Source: Helicobacter pylori, Rattus norvegicus, Escherichia coli
Sequence:

MGSSHHHHHH SSGLVPRGSH MRDYSELEIF EGNPLDKWND IIFHASKKAS KKELERLLEL LALCETFIEK EDLEEKFESF AKALRIDEEL QQKIESRKTD IVIQSMANIL SALFMDEFFE QVEEIRGFID KIAENVEEVK RKHSAILASP NPDEKTKEEL EELMSDIKKT ANKVRSKLKS IEQSIEQEEG LNRSSADLRI RKTQHSTLSR KFVEVMSEYN ATQSDYGSGS GRHQEWLRFV DLLKNAYQND LHLPLLNLML TPDEREALGT RVRIVEELLR GEMSQRELKN ELGAGIATIT RGSNSLKAAP VELRQWLEEV LLKSD

Experimental information

• Beam: Instrument name: Nara Institute of Science and Technology Rigaku Nano-Viewer; City: Ikoma / 国: Japan / Type of source: X-ray in house / Wavelength: 0.15418 Å / Dist. spec. to detc.: 0.75 mm
• Detector: Name: Pilatus 200K / Type: Pilatus / Pixsize x: 172 mm

Scan

Title: HP2042 form from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, Trp repressor from Escherichia coli (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:1WRT))
Measurement date: Dec 8, 2016 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 60 sec. / Number of frames: 25 / Unit: 1/A /

	Min	Max
Q	0.0138	0.3003

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 220 /

	Min	Max
Q	0.01382	0.215586
P(R) point	1	220
R	0	200

Result

Type of curve: extrapolated

	Experimental	Standard	Standard error	Porod
MW	177 kDa	177 kDa	4	237 kDa
Volume	-	-	-	379 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	37.39	0.9	37.24	1.5
Radius of gyration, Rg	5.24 nm	2	5.11 nm	0.3

	Min	Max
D	-	20
Guinier point	1	10