Browse by MODEL: Hybrid

SASDUR2 – SB24-nnn (coiled coil protein origami irregular octahedron assembled from three linear chains)

SB6 (Linear coiled-coil protein origami structure consisting of 6 coiled-coil forming segments)SB9b (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments)SB9c (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments) experimental SAS data
MODELLER model
Sample: SB6 (Linear coiled-coil protein origami structure consisting of 6 coiled-coil forming segments) monomer, 26 kDa synthetic construct protein
SB9b (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments) monomer, 42 kDa synthetic construct protein
SB9c (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments) monomer, 41 kDa synthetic construct protein
Buffer: 20 mM Tris, 150 mM NaCL, 3% glycerol, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Oct 25
Preorganized cyclic modules facilitate the self-assembly of protein nanostructures Chemical Science (2024)
Snoj J, Lapenta F, Jerala R
RgGuinier 4.8 nm
Dmax 16.1 nm
VolumePorod 443 nm3

SASDUS2 – SB24-ncn (coiled coil protein origami irregular octahedron assembled from 2 linear chains and 1 cyclic chain)

SB9b (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments)SB9c (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments)cySB6 (Cyclic coiled-coil protein origami structure consisting of 6 coiled-coil forming segments) experimental SAS data
COOT model
Sample: SB9b (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments) monomer, 42 kDa synthetic construct protein
SB9c (Linear coiled-coil protein origami structure consisting of 9 coiled-coil forming segments) monomer, 41 kDa synthetic construct protein
CySB6 (Cyclic coiled-coil protein origami structure consisting of 6 coiled-coil forming segments) monomer, 26 kDa synthetic construct protein
Buffer: 20 mM Tris, 150 mM NaCL, 3% glycerol, 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 9
Preorganized cyclic modules facilitate the self-assembly of protein nanostructures Chemical Science (2024)
Snoj J, Lapenta F, Jerala R
RgGuinier 4.7 nm
Dmax 14.7 nm
VolumePorod 428 nm3

SASDRR7 – Radical SAM enzyme peptide epimerase in the presence of SAM (S-adenosyl-L-methionine) and a peptide subtrate

Putative peptide biosynthesis protein YydG experimental SAS data
DADIMODO model
Sample: Putative peptide biosynthesis protein YydG dimer, 80 kDa Bacillus subtilis (strain … protein
Buffer: 25 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2022 Nov 30
Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol (2023)
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A
RgGuinier 2.9 nm
Dmax 12.0 nm
VolumePorod 113 nm3

SASDRS7 – Radical SAM enzyme peptide epimerase in the presence of SAM (S-adenosyl-L-methionine)

Putative peptide biosynthesis protein YydG experimental SAS data
DADIMODO model
Sample: Putative peptide biosynthesis protein YydG dimer, 80 kDa Bacillus subtilis (strain … protein
Buffer: 25 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2022 Nov 29
Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol (2023)
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A
RgGuinier 2.9 nm
Dmax 11.8 nm
VolumePorod 115 nm3

SASDHZ9 – Condensin complex subunit 1, Ycs4

Condensin complex subunit 1 experimental SAS data
MONSA model
Sample: Condensin complex subunit 1 monomer, 137 kDa Chaetomium thermophilum protein
Buffer: 25 mM Tris, 300 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Nov 20
Molecular flexibility of the condensin subunit Ycs4 is modulated by kleisin binding
Karen Manalastas-Cantos
RgGuinier 5.2 nm
Dmax 17.7 nm
VolumePorod 296 nm3

SASDJ22 – Condensin complex subunit 1 (Ycs4) bound to condensin complex subunit 2, 336-418 (Brn1S)

Condensin complex subunit 1Condensin complex subunit 2, 336-418 experimental SAS data
MONSA model
Sample: Condensin complex subunit 1 monomer, 137 kDa Chaetomium thermophilum protein
Condensin complex subunit 2, 336-418 monomer, 9 kDa Chaetomium thermophilum protein
Buffer: 25 mM Tris, 300 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Nov 20
Molecular flexibility of the condensin subunit Ycs4 is modulated by kleisin binding
Karen Manalastas-Cantos
RgGuinier 5.0 nm
Dmax 16.9 nm
VolumePorod 279 nm3

SASDJ32 – Condensin complex subunit 1 (Ycs4) bound to condensin complex subunit 2, 225-418 (Brn1L)

Condensin complex subunit 1Condensin complex subunit 2, 225-418 experimental SAS data
MONSA model
Sample: Condensin complex subunit 1 monomer, 137 kDa Chaetomium thermophilum protein
Condensin complex subunit 2, 225-418 monomer, 21 kDa Chaetomium thermophilum protein
Buffer: 25 mM Tris, 300 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Nov 20
Molecular flexibility of the condensin subunit Ycs4 is modulated by kleisin binding
Karen Manalastas-Cantos
RgGuinier 4.9 nm
Dmax 15.9 nm
VolumePorod 309 nm3

SASDJ42 – Pentameric assembly of condensin complex subunits 1 and 2 (Ycs4-Brn1L-Brn1C) with subunits of the SMC hinge domain-containing protein (Smc4hd)

Condensin complex subunit 1Condensin complex subunit 2, 225-418Condensin complex subunit 2, 776-898SMC hinge domain-containing protein, 263-466SMC hinge domain-containing protein, 1367-1542 experimental SAS data
MONSA model
Sample: Condensin complex subunit 1 monomer, 137 kDa Chaetomium thermophilum protein
Condensin complex subunit 2, 225-418 monomer, 21 kDa Chaetomium thermophilum protein
Condensin complex subunit 2, 776-898 monomer, 14 kDa Chaetomium thermophilum protein
SMC hinge domain-containing protein, 263-466 monomer, 22 kDa Chaetomium thermophilum protein
SMC hinge domain-containing protein, 1367-1542 monomer, 20 kDa Chaetomium thermophilum protein
Buffer: 25 mM Tris, 300 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Nov 20
Molecular flexibility of the condensin subunit Ycs4 is modulated by kleisin binding
Karen Manalastas-Cantos
RgGuinier 5.1 nm
Dmax 17.9 nm
VolumePorod 355 nm3

SASDSQ9 – NanoLuc luciferase

Oplophorus-luciferin 2-monooxygenase catalytic subunit experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Oplophorus-luciferin 2-monooxygenase catalytic subunit monomer, 20 kDa Oplophorus gracilirostris protein
Buffer: 10 mM Tris-HCl, 50 mM NaCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2021 May 27
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun 14(1):7864 (2023)
Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M
RgGuinier 1.8 nm
Dmax 5.9 nm
VolumePorod 38 nm3

SASDLM3 – Interleukin-11 signalling complex, truncated gp130

Interleukin-6 receptor subunit betaInterleukin-11Interleukin-11 receptor subunit alpha experimental SAS data
OTHER model
Sample: Interleukin-6 receptor subunit beta dimer, 69 kDa Homo sapiens protein
Interleukin-11 dimer, 36 kDa Homo sapiens protein
Interleukin-11 receptor subunit alpha dimer, 64 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 0.2% sodium azide, pH: 8.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2019 Jun 8
Structures of the interleukin 11 signalling complex reveal gp130 dynamics and the inhibitory mechanism of a cytokine variant Nature Communications 14(1) (2023)
Metcalfe R, Hanssen E, Fung K, Aizel K, Kosasih C, Zlatic C, Doughty L, Morton C, Leis A, Parker M, Gooley P, Putoczki T, Griffin M
RgGuinier 5.3 nm
Dmax 17.6 nm
VolumePorod 405 nm3