MACROMOLECULE TYPE: heterocomplex

SASDQV5 – NPL3 protein RNA recognition motifs 1 and 2 (RRM1,2) wild-type, bound to RNA

Serine/arginine (SR)-type shuttling mRNA binding protein NPL3Short RNA oligonucleotide (NPL3 binding sequence) experimental SAS data
Serine/arginine (SR)-type shuttling mRNA binding protein NPL3 Short RNA oligonucleotide (NPL3 binding sequence) Kratky plot
Sample: Serine/arginine (SR)-type shuttling mRNA binding protein NPL3 monomer, 18 kDa Saccharomyces cerevisiae (strain … protein
Short RNA oligonucleotide (NPL3 binding sequence) monomer, 4 kDa RNA
Buffer: 20 mM NaPO4, 50 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, SFB 1035, Technische Universität München on 2020 Feb 20
Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Res (2022)
Keil P, Wulf A, Kachariya N, Reuscher S, Hühn K, Silbern I, Altmüller J, Keller M, Stehle R, Zarnack K, Sattler M, Urlaub H, Sträßer K
RgGuinier 2.0 nm
Dmax 6.3 nm
VolumePorod 30 nm3

SASDMH9 – Pseudomonas aeruginosa Multidrug resistance operon repressor (MexR) in complex with 34bp dsDNA binding sequence (SANS data at 0% D2O)

Multidrug resistance operon repressor34 base pair double-stranded DNA experimental SAS data
MONSA model
Sample: Multidrug resistance operon repressor dimer, 32 kDa Pseudomonas aeruginosa protein
34 base pair double-stranded DNA monomer, 21 kDa synthetic construct DNA
Buffer: 20mM NaPO4, 150 mM NaCl, 10 mM DTT, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2018 May 30
Small-angle X-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model Biophysical Journal (2022)
Caporaletti F, Pietras Z, Morad V, Mårtensson L, Gabel F, Wallner B, Martel A, Sunnerhagen M
RgGuinier 2.9 nm
Dmax 7.8 nm
VolumePorod 79 nm3

SASDFH6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex in the presence of DNA substrate

Probable exodeoxyribonuclease III protein XthADNA ligase ABeta sliding clampDNA ligase A nicked DNA substrate experimental SAS data
DAMMIF model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
DNA ligase A nicked DNA substrate dimer, 16 kDa DNA
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 5.8 nm
Dmax 19.1 nm
VolumePorod 496 nm3

SASDNH7 – Tn3 resolvase dimer bound to site II DNA sequence

Transposon Tn3 resolvaseTn3 res, resolvase binding site II experimental SAS data
CUSTOM IN-HOUSE model
Sample: Transposon Tn3 resolvase dimer, 43 kDa Escherichia coli protein
Tn3 res, resolvase binding site II monomer, 32 kDa DNA
Buffer: 25 mM Tris, 150 mM NaCl, 10 mM MgCl2, 1% glycerol, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Nov 6
Structural basis for topological regulation of Tn3 resolvase. Nucleic Acids Res (2022)
Montaño SP, Rowland SJ, Fuller JR, Burke ME, MacDonald AI, Boocock MR, Stark WM, Rice PA
RgGuinier 5.0 nm
Dmax 14.9 nm
VolumePorod 217 nm3

SASDMZ6 – single-stranded DNA dC->dU-editing enzyme APOBEC3G full length in complex with DNA: tetramer

DNA dC->dU-editing enzyme APOBEC-3G40-mer single stranded inhibitory DNA experimental SAS data
DAMFILT model
Sample: DNA dC->dU-editing enzyme APOBEC-3G tetramer, 186 kDa Homo sapiens protein
40-mer single stranded inhibitory DNA dimer, 24 kDa DNA
Buffer: 50 mM phosphate pH 6.0, 200 mM NaCl, 2 mM β-mercaptoethanol (β-ME), 5% glycerol, 200 µM Na2-EDTA, pH: 6
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2019 Aug 6
Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity Viruses 14(9):1974 (2022)
Barzak F, Ryan T, Mohammadzadeh N, Harjes S, Kvach M, Kurup H, Krause K, Chelico L, Filichev V, Harjes E, Jameson G
RgGuinier 4.7 nm
Dmax 16.2 nm
VolumePorod 395 nm3

SASDM27 – single-stranded DNA dC->dU-editing enzyme APOBEC3G full length in complex with DNA: monomer

40-mer single stranded inhibitory DNADNA dC->dU-editing enzyme APOBEC-3G experimental SAS data
DAMFILT model
Sample: 40-mer single stranded inhibitory DNA monomer, 12 kDa DNA
DNA dC->dU-editing enzyme APOBEC-3G monomer, 46 kDa Homo sapiens protein
Buffer: 50 mM phosphate pH 6.0, 200 mM NaCl, 2 mM β-mercaptoethanol (β-ME), 5% glycerol, 200 µM Na2-EDTA, pH: 6
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2019 Aug 6
Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity Viruses 14(9):1974 (2022)
Barzak F, Ryan T, Mohammadzadeh N, Harjes S, Kvach M, Kurup H, Krause K, Chelico L, Filichev V, Harjes E, Jameson G
RgGuinier 3.1 nm
Dmax 10.0 nm
VolumePorod 118 nm3

SASDNP7 – Translation initiation factor 2 (aIF2)-tRNA complex in Gd-HPDO3A

Translation initiation factor 2 subunit gammaTranslation initiation factor 2 subunit alphatransfer RNA experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Translation initiation factor 2 subunit gamma monomer, 46 kDa Saccharolobus solfataricus (strain … protein
Translation initiation factor 2 subunit alpha monomer, 10 kDa Saccharolobus solfataricus (strain … protein
Transfer RNA monomer, 23 kDa Escherichia coli RNA
Buffer: 10 mM MOPS- NaOH pH 6.7, 200 mM NaCl, 5 mM MgCl 2, 1 mM GDPNP, pH: 6.7
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Nov 26
Medical contrast agents as promising tools for biomacromolecular SAXS experiments. Acta Crystallogr D Struct Biol 78(Pt 9):1120-1130 (2022)
Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E
RgGuinier 3.6 nm
Dmax 13.0 nm
VolumePorod 102 nm3

SASDMD9 – 7SK small nuclear RNA stem loop-1 bound to the arginine rich motif of HIV-1 Tat Group M, Subtype G

Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNAProtein Tat experimental SAS data
Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA Protein Tat Kratky plot
Sample: Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA monomer, 18 kDa Homo sapiens RNA
Protein Tat monomer, 2 kDa Human immunodeficiency virus … protein
Buffer: 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA, pH: 5.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 27
A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Commun Biol 5(1):819 (2022)
Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM
RgGuinier 2.5 nm
Dmax 9.9 nm
VolumePorod 28 nm3

SASDME9 – 7SK stem-loop 1 with HEXIM Arginine Rich Motif

Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNAProtein HEXIM1 experimental SAS data
Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA Protein HEXIM1 Kratky plot
Sample: Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA monomer, 18 kDa Homo sapiens RNA
Protein HEXIM1 monomer, 2 kDa Homo sapiens protein
Buffer: 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA, pH: 5.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 27
A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Commun Biol 5(1):819 (2022)
Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM
RgGuinier 2.2 nm
Dmax 8.2 nm
VolumePorod 26 nm3

SASDMF9 – 7SK small nuclear RNA stem loop-1 bound to the arginine rich motif of HIV-1 Tat Group M, Subtype B (Isolate A18188)

Protein TatHomo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA experimental SAS data
Protein Tat Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA Kratky plot
Sample: Protein Tat monomer, 2 kDa Human immunodeficiency virus … protein
Homo sapiens RNA component of 7SK nuclear ribonucleoprotein (RN7SK), small nuclear RNA monomer, 18 kDa Homo sapiens RNA
Buffer: 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA, pH: 5.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Sep 9
A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Commun Biol 5(1):819 (2022)
Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM
RgGuinier 2.3 nm
Dmax 9.7 nm
VolumePorod 28 nm3