Browse by MODEL: Ab initio only

SASDJJ9 – M100 DNA oligonucleotide bound to the protein fusion of Insulin gene enhancer protein Isl-1 homeodomain/LIM-interaction domain (Isl1-HDLID) and LIM/homeobox protein Lhx3 LIM-homeodomain (Lhx3-LIMHD): M100 + 2HDLL

M100 oligonucleotideInsulin gene enhancer protein ISL-1LIM/homeobox protein Lhx3 experimental SAS data
MONSA model
Sample: M100 oligonucleotide monomer, 12 kDa DNA
Insulin gene enhancer protein ISL-1 monomer, 14 kDa Mus musculus protein
LIM/homeobox protein Lhx3 monomer, 23 kDa Mus musculus protein
Buffer: 20 mM sodium phosphate monobasic/dibasic, 100 mM NaCl, 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Nov 2
Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification Journal of Structural Biology: X :100043 (2020)
Smith N, Wilkinson-White L, Kwan A, Trewhella J, Matthews J
RgGuinier 3.6 nm
Dmax 14.0 nm
VolumePorod 70 nm3

SASDJK9 – M100 DNA oligonucleotide

M100 oligonucleotide experimental SAS data
MONSA model
Sample: M100 oligonucleotide monomer, 12 kDa DNA
Buffer: 20 mM sodium phosphate monobasic/dibasic, 100 mM NaCl, 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Nov 2
Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification Journal of Structural Biology: X :100043 (2020)
Smith N, Wilkinson-White L, Kwan A, Trewhella J, Matthews J
RgGuinier 1.9 nm
Dmax 6.8 nm
VolumePorod 15 nm3

SASDJZ7 – A modular diphtheria toxin/flavohemoprotein nanotransporter (MNT) fused to an epidermal growth factor ligand module (MNT-EGF)

Modular nanotransporter with an epidermal growth factor ligand module experimental SAS data
GASBOR model
Sample: Modular nanotransporter with an epidermal growth factor ligand module monomer, 76 kDa synthetic construct protein
Buffer: 150 mM NaCl, 10 mM phosphate buffer saline, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 24
Low-resolution structures of modular nanotransporters shed light on their functional activity Acta Crystallographica Section D Structural Biology 76(12):1270-1279 (2020)
Khramtsov Y, Vlasova A, Vlasov A, Rosenkranz A, Ulasov A, Ryzhykau Y, Kuklin A, Orekhov A, Eydlin I, Georgiev G, Gordeliy V, Sobolev A
RgGuinier 4.2 nm
Dmax 16.0 nm
VolumePorod 161 nm3

SASDJV7 – pri-miR16-1 primary microRNA

primary microRNA pri-miR16-1 experimental SAS data
DAMMIF model
Sample: Primary microRNA pri-miR16-1 monomer, 36 kDa Homo sapiens RNA
Buffer: 50 mM KCl, 50 mM HEPES, 5 mM DTT, 1% glycerol, pH: 7.5
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2017 Apr 12
Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures Biophysical Journal (2020)
Pabit S, Chen Y, Usher E, Cook E, Pollack L, Showalter S
RgGuinier 4.4 nm
Dmax 17.2 nm
VolumePorod 74 nm3

SASDJW7 – pri-miR16-1 primary microRNA in complex with DGCR8-core protein

primary microRNA pri-miR16-1 complexed with DGCR8-core proteinMicroprocessor complex subunit DGCR8 experimental SAS data
DAMMIF model
Sample: Primary microRNA pri-miR16-1 complexed with DGCR8-core protein monomer, 36 kDa Homo sapiens RNA
Microprocessor complex subunit DGCR8 monomer, 26 kDa Homo sapiens protein
Buffer: 50 mM KCl, 50 mM HEPES, 5 mM DTT, 1% glycerol, 50% sucrose, DGCR8-core, pH: 7.5
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2017 Apr 12
Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures Biophysical Journal (2020)
Pabit S, Chen Y, Usher E, Cook E, Pollack L, Showalter S
RgGuinier 5.0 nm
Dmax 17.2 nm
VolumePorod 125 nm3

SASDNW3 – Fibrillin-1 fragment PF2 crosslinked to tropoelastin by transglutaminase 2

Fibrillin-1Elastin experimental SAS data
DAMMIF model
Sample: Fibrillin-1 monomer, 44 kDa Homo sapiens protein
Elastin monomer, 60 kDa Homo sapiens protein
Buffer: Tris buffered saline, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Feb 21
Transglutaminase-Mediated Cross-Linking of Tropoelastin to Fibrillin Stabilises the Elastin Precursor Prior to Elastic Fibre Assembly. J Mol Biol 432(21):5736-5751 (2020)
Lockhart-Cairns MP, Newandee H, Thomson J, Weiss AS, Baldock C, Tarakanova A
RgGuinier 7.1 nm
Dmax 23.5 nm

SASDHR5 – Heat shock protein 40, subfamily A (PfHSP40)

HSP40, subfamily A experimental SAS data
DAMMIF model
Sample: HSP40, subfamily A dimer, 97 kDa Plasmodium falciparum protein
Buffer: 50 mM Tris, 5 mM MgCl2, 300 mM KCl, 1 mM β-mercaptoethanol, 5% glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Oct 24
Structural-functional diversity of malaria parasite's PfHSP70-1 and PfHSP40 chaperone pair gives an edge over human orthologs in chaperone-assisted protein folding. Biochem J 477(18):3625-3643 (2020)
Anas M, Shukla A, Tripathi A, Kumari V, Prakash C, Nag P, Kumar LS, Sharma SK, Ramachandran R, Kumar N
RgGuinier 4.3 nm
Dmax 15.0 nm
VolumePorod 339 nm3

SASDHU5 – Heat shock protein 70 (PfHSP70-1)

Heat shock protein 70Peptide experimental SAS data
DAMFILT model
Sample: Heat shock protein 70 monomer, 74 kDa Plasmodium falciparum protein
Peptide monomer, 1 kDa synthetic construct protein
Buffer: 50mM Tris, 5mM MgCl2, 500mM KCl, 5mM Bme, 5% glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Oct 24
Structural-functional diversity of malaria parasite's PfHSP70-1 and PfHSP40 chaperone pair gives an edge over human orthologs in chaperone-assisted protein folding. Biochem J 477(18):3625-3643 (2020)
Anas M, Shukla A, Tripathi A, Kumari V, Prakash C, Nag P, Kumar LS, Sharma SK, Ramachandran R, Kumar N
RgGuinier 5.3 nm
Dmax 16.6 nm
VolumePorod 450 nm3

SASDJW9 – Mammalian cell entry protein 4A (Mce4A36-400)

Mce-family protein Mce4An-Dodecyl-β-D-Maltopyranoside experimental SAS data
OTHER model
Sample: Mce-family protein Mce4A monomer, 44 kDa Mycobacterium tuberculosis (strain … protein
N-Dodecyl-β-D-Maltopyranoside 0, 102 kDa
Buffer: 50mM Tris, 500mM NaCl, 10% Glycerol, 5mM DDM, 1mM Beta-ME, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 May 13
Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis IUCrJ 8(5) (2021)
Asthana P, Singh D, Pedersen J, Hynönen M, Sulu R, Murthy A, Laitaoja M, Jänis J, Riley L, Venkatesan R
RgGuinier 5.7 nm
Dmax 21.5 nm
VolumePorod 446 nm3

SASDJX9 – Mammalian cell entry protein 4A (Mce4A121-400)

n-Dodecyl-β-D-MaltopyranosideMce-family protein Mce4A experimental SAS data
CUSTOM IN-HOUSE model
Sample: N-Dodecyl-β-D-Maltopyranoside 0, 102 kDa
Mce-family protein Mce4A monomer, 35 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 50mM Tris, 500mM NaCl, 10% Glycerol, 5mM DDM, 1mM Beta-ME, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Nov 28
Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis IUCrJ 8(5) (2021)
Asthana P, Singh D, Pedersen J, Hynönen M, Sulu R, Murthy A, Laitaoja M, Jänis J, Riley L, Venkatesan R
RgGuinier 5.0 nm
Dmax 19.1 nm
VolumePorod 278 nm3