Browse by MODEL: Hybrid

SASDDB5 – MsbA in stealth nanodisc (SANS, 100% D2O)

Lipid A export ATP-binding/permease protein MsbAMembrane scaffold protein 1D1 (deuterated, 75%)1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphocholine (deuteration: 78% head, 92% acyl) experimental SAS data
SASREF CV model
Sample: Lipid A export ATP-binding/permease protein MsbA dimer, 133 kDa Escherichia coli protein
Membrane scaffold protein 1D1 (deuterated, 75%) dimer, 49 kDa protein
1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphocholine (deuteration: 78% head, 92% acyl), 1 kDa Escherichia coli
Buffer: 30 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SANS data collected at D11, ILL on 2017 Mar 9
Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs. Structure 26(8):1072-1079.e4 (2018)
Josts I, Nitsche J, Maric S, Mertens HD, Moulin M, Haertlein M, Prevost S, Svergun DI, Busch S, Forsyth VT, Tidow H
RgGuinier 4.0 nm
Dmax 13.0 nm
VolumePorod 189 nm3

SASDDJ9 – Conformation of the R1-3 human dystrophin fragment (SANS)

R1-3 human dystrophin fragment experimental SAS data
YASARA model
Sample: R1-3 human dystrophin fragment monomer, 39 kDa Homo sapiens protein
Buffer: 20 mM Tris-d11, 150 mM NaCl, 0.1 mM EDTA-d16, in 100% D2O, pD 7.5, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2016 Nov 7
Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids. Biophys J 115(7):1231-1239 (2018)
Dos Santos Morais R, Delalande O, Pérez J, Mias-Lucquin D, Lagarrigue M, Martel A, Molza AE, Chéron A, Raguénès-Nicol C, Chenuel T, Bondon A, Appavou MS, Le Rumeur E, Combet S, Hubert JF
RgGuinier 4.2 nm
Dmax 17.7 nm
VolumePorod 46 nm3

SASDDL9 – Conformation of R1-3 human dystrophin fragment in interaction with anionic phospholipid bicelles (SANS)

R1-3 human dystrophin fragment experimental SAS data
YASARA model
Sample: R1-3 human dystrophin fragment monomer, 39 kDa Homo sapiens protein
Buffer: 20 mM Tris-d11, 150 mM NaCl, 0.1 mM EDTA-d16, in 100% D2O, pD 7.5, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2016 Nov 7
Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids. Biophys J 115(7):1231-1239 (2018)
Dos Santos Morais R, Delalande O, Pérez J, Mias-Lucquin D, Lagarrigue M, Martel A, Molza AE, Chéron A, Raguénès-Nicol C, Chenuel T, Bondon A, Appavou MS, Le Rumeur E, Combet S, Hubert JF
RgGuinier 6.2 nm
Dmax 24.8 nm
VolumePorod 100 nm3

SASDEM4 – HrpG/HrpV/HrpJ gatekeeper complex from Erwinia amylovora

Type III secretion protein HrpGType III secretion protein HrpVHypersensitivity response secretion protein HrpJ experimental SAS data
CORAL model
Sample: Type III secretion protein HrpG, 19 kDa Erwinia amylovora protein
Type III secretion protein HrpV, 13 kDa Erwinia amylovora protein
Hypersensitivity response secretion protein HrpJ, 42 kDa Erwinia amylovora protein
Buffer: 20mM Tris-Cl, pH 8.0, 100mM NaCl, 2mM DTT, 0.5mM EDTA, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Apr 3
Migration of Type III Secretion System Transcriptional Regulators Links Gene Expression to Secretion. MBio 9(4) (2018)
Charova SN, Gazi AD, Mylonas E, Pozidis C, Sabarit B, Anagnostou D, Psatha K, Aivaliotis M, Beuzon CR, Panopoulos NJ, Kokkinidis M
RgGuinier 4.0 nm
Dmax 16.0 nm

SASDDF7 – Armless mitochondrial tRNA-Arg from Romanomermis culicivorax

Arginyl transfer RNA experimental SAS data
PYMOL model
Sample: Arginyl transfer RNA monomer, 13 kDa Romanomermis culicivorax RNA
Buffer: 50 mM HEPES-NaOH 10 mM MgCl2, pH: 7.4
Experiment: SAXS data collected at SWING, SOLEIL on 2015 Dec 16
Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res (2018)
Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M
RgGuinier 2.1 nm
Dmax 6.7 nm
VolumePorod 20 nm3

SASDDG7 – Armless mitochondrial tRNA-Ile from Romanomermis culicivorax

Isoleucyl transfer RNA experimental SAS data
PYMOL model
Sample: Isoleucyl transfer RNA monomer, 15 kDa Romanomermis culicivorax RNA
Buffer: 50 mM HEPES-NaOH 10 mM MgCl2, pH: 7.4
Experiment: SAXS data collected at SWING, SOLEIL on 2015 Dec 16
Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res (2018)
Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M
RgGuinier 2.0 nm
Dmax 6.7 nm
VolumePorod 20 nm3

SASDCR9 – Kif2A-tubulin-DARP complex in the presence of AMP-PNP

Designed Ankyrin Repeat Protein D1Kinesin-like protein KIF2ATubulin alpha-1B chainTubulin beta-2B chain experimental SAS data
DAMMIF model
Sample: Designed Ankyrin Repeat Protein D1 monomer, 18 kDa synthetic construct protein
Kinesin-like protein KIF2A monomer, 48 kDa Homo sapiens protein
Tubulin alpha-1B chain dimer, 100 kDa Bos taurus protein
Tubulin beta-2B chain dimer, 100 kDa Bos taurus protein
Buffer: HEPES 20 mM, MgCl2 1mM, NaCl 150mM, pH: 7.2
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2016 May 16
Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate. Nat Commun 9(1):2628 (2018)
Trofimova D, Paydar M, Zara A, Talje L, Kwok BH, Allingham JS
RgGuinier 5.4 nm
Dmax 19.5 nm
VolumePorod 374 nm3

SASDDT4 – Fc region of Immunoglobulin G1 (IgG1 Fc)

Immunoglobulin heavy constant gamma 1 experimental SAS data
BILBOMD model
Sample: Immunoglobulin heavy constant gamma 1 dimer, 53 kDa Homo sapiens protein
Buffer: 20mM HEPES, 50mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Feb 17
Conformational Plasticity of the Immunoglobulin Fc Domain in Solution. Structure 26(7):1007-1014.e2 (2018)
Remesh SG, Armstrong AA, Mahan AD, Luo J, Hammel M
RgGuinier 2.6 nm
Dmax 10.0 nm
VolumePorod 70 nm3

SASDDU4 – Fc region of Immunoglobulin G2 (IgG2 Fc)

Immunoglobulin heavy constant gamma 2 experimental SAS data
BILBOMD model
Sample: Immunoglobulin heavy constant gamma 2 dimer, 52 kDa Homo sapiens protein
Buffer: 20mM HEPES, 50mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Feb 17
Conformational Plasticity of the Immunoglobulin Fc Domain in Solution. Structure 26(7):1007-1014.e2 (2018)
Remesh SG, Armstrong AA, Mahan AD, Luo J, Hammel M
RgGuinier 2.8 nm
Dmax 9.0 nm
VolumePorod 67 nm3

SASDDV4 – Fc-region of Immunoglobulin G1, M135Y/S137T/T139E mutant (IgG1 Fc-YTE)

Immunoglobulin heavy constant gamma 1 M255Y/S257T/T259E experimental SAS data
BILBOMD model
Sample: Immunoglobulin heavy constant gamma 1 M255Y/S257T/T259E dimer, 53 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 50mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Feb 17
Conformational Plasticity of the Immunoglobulin Fc Domain in Solution. Structure 26(7):1007-1014.e2 (2018)
Remesh SG, Armstrong AA, Mahan AD, Luo J, Hammel M
RgGuinier 2.7 nm
Dmax 10.0 nm
VolumePorod 74 nm3