SASDFS4: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A...

Basic information

• Entry: Database: SASBDB / ID: SASDFS4

Sample

HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))

• HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (protein), Fusion protein2, Helicobacter pylori, Rattus norvegicus, de novo design

• Biological species: Helicobacter pylori (bacteria); Rattus norvegicus (Norway rat); de novo design (unknown)
• 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 #2930: ; Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 0.10 / P-value: 0.000088; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL)); Specimen concentration: 1.90-6.80
• Buffer: Name: 20 mM Tris-HCl 150 mM NaCl / pH: 8

Entity #1583

Name: Fusion protein2 / Type: protein
Description: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain
Formula weight: 29.855 / Num. of mol.: 6
Source: Helicobacter pylori, Rattus norvegicus, de novo design
Sequence:

MGSSHHHHHH SSGLVPRGSH MRDYSELEIF EGNPLDKWND IIFHASKKAS KKELERLLEL LALCETFIEK EDLEEKFESF AKALRIDEEL QQKIESRKTD IVIQSMANIL SALFMDEFFE QVEEIRGFID KIAENVEEVK RKHSAILASP NPDEKTKEEL EELMSDIKKT ANKVRSKLKS IEQSIEQEEG LNRSSADLRI RKTQHSTLSR KFVEVMSEYN ATQSDYGSGG EIAAIKQEIA AIKKEIAAIK WEIAAIKQGY G

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: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))
Measurement date: Mar 29, 2017 / 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: 218 /

	Min	Max
Q	0.015662	0.215586
P(R) point	1	218
R	0	240

Result

Type of curve: extrapolated

	Experimental	Standard	Standard error	Porod
MW	187 kDa	187 kDa	10	401 kDa
Volume	-	-	-	642 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	40.9	2.2	40.11	3.11
Radius of gyration, Rg	7 nm	0.3	6.53 nm	0.6

	Min	Max
D	-	24
Guinier point	1	8