Browse by MODEL: Hybrid

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

SASDN75 – TetR/AcrR-like repressor SCO3201 from Streptomyces coelicor

Putative tetR-family transcriptional regulator experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Putative tetR-family transcriptional regulator dimer, 47 kDa Streptomyces coelicolor (strain … protein
Buffer: 20 mM Tris/HCl, 400 mM NaCl, 50 mM imidazole, 1 mM DTT, pH: 8.5
Experiment: SAXS data collected at BM29, ESRF on 2014 May 2
Crystal Structures of Free and Ligand-Bound Forms of the TetR/AcrR-Like Regulator SCO3201 from Streptomyces coelicolor Suggest a Novel Allosteric Mechanism. FEBS J (2022)
Werten S, Waack P, Palm GJ, Virolle MJ, Hinrichs W
RgGuinier 2.6 nm
Dmax 6.5 nm
VolumePorod 77 nm3

SASDPZ3 – Complex of XPA1-239 and RPAΔ32NΔ70N complex engaged on 3’ss-ds DNA junction NER substrate

DNA repair protein complementing XP-A cellsReplication protein A 70 kDa DNA-binding subunitReplication protein A 32 kDa subunitReplication protein A 14 kDa subunit3-prime ss-ds DNA junction NER model substrate experimental SAS data
MES-FOXS model
Sample: DNA repair protein complementing XP-A cells monomer, 27 kDa Homo sapiens protein
Replication protein A 70 kDa DNA-binding subunit monomer, 49 kDa Homo sapiens protein
Replication protein A 32 kDa subunit monomer, 25 kDa Homo sapiens protein
Replication protein A 14 kDa subunit monomer, 14 kDa Homo sapiens protein
3-prime ss-ds DNA junction NER model substrate monomer, 17 kDa DNA
Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 2% glycerol, 1 mM DTT, pH: 8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Mar 4
Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair Proceedings of the National Academy of Sciences 119(34) (2022)
Kim M, Kim H, D’Souza A, Gallagher K, Jeong E, Topolska-Wós A, Ogorodnik Le Meur K, Tsai C, Tsai M, Kee M, Tainer J, Yeo J, Chazin W, Schärer O
RgGuinier 4.3 nm
Dmax 14.7 nm
VolumePorod 189 nm3

SASDP24 – Complex of XPA1-239 and RPAΔ32NΔ70N complex engaged on 5’ss-ds DNA junction NER substrate

Replication protein A 14 kDa subunitDNA repair protein complementing XP-A cellsReplication protein A 70 kDa DNA-binding subunitReplication protein A 32 kDa subunit5-prime ss-ds DNA junction NER model substrate experimental SAS data
MES-FOXS model
Sample: Replication protein A 14 kDa subunit monomer, 14 kDa Homo sapiens protein
DNA repair protein complementing XP-A cells monomer, 27 kDa Homo sapiens protein
Replication protein A 70 kDa DNA-binding subunit monomer, 49 kDa Homo sapiens protein
Replication protein A 32 kDa subunit monomer, 25 kDa Homo sapiens protein
5-prime ss-ds DNA junction NER model substrate monomer, 17 kDa DNA
Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 2% glycerol, 1 mM DTT, pH: 8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Mar 4
Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair Proceedings of the National Academy of Sciences 119(34) (2022)
Kim M, Kim H, D’Souza A, Gallagher K, Jeong E, Topolska-Wós A, Ogorodnik Le Meur K, Tsai C, Tsai M, Kee M, Tainer J, Yeo J, Chazin W, Schärer O
RgGuinier 4.6 nm
Dmax 16.5 nm
VolumePorod 220 nm3

SASDNY3 – Calcium-bound Calmodulin complexed with Calmidazolium

Calmodulin-1Calmidazolium experimental SAS data
Sample: Calmodulin-1 monomer, 17 kDa Homo sapiens protein
Calmidazolium monomer, 1 kDa
Buffer: 20 mM Hepes, 150 mM NaCl, 2 mM CaCl2, pH: 7.4
Experiment: SAXS data collected at SWING, SOLEIL on 2020 Nov 15
Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. BMC Biol 20(1):176 (2022)
Léger C, Pitard I, Sadi M, Carvalho N, Brier S, Mechaly A, Raoux-Barbot D, Davi M, Hoos S, Weber P, Vachette P, Durand D, Haouz A, Guijarro JI, Ladant D, Chenal A
RgGuinier 1.7 nm
Dmax 5.2 nm
VolumePorod 30 nm3

SASDNT5 – Bradyzoite Pseudokinase 1 (amino acids 61-377)

Rhoptry kinase family protein experimental SAS data
Sample: Rhoptry kinase family protein tetramer, 143 kDa Toxoplasma gondii (strain … protein
Buffer: 20 mM HEPES, 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Apr 19
Divergent kinase WNG1 is regulated by phosphorylation of an atypical activation sub-domain. Biochem J (2022)
Dewangan PS, Beraki TG, Paiz EA, Appiah Mensah D, Chen Z, Reese ML
RgGuinier 3.8 nm
Dmax 11.5 nm
VolumePorod 207 nm3

SASDHB5 – RelA Homology Domain of p50/RelA heterodimer

NF-kappa-B p105 subunit 39-350Transcription factor p65 19-321 experimental SAS data
MULTIFOXS model
Sample: NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Transcription factor p65 19-321 monomer, 35 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 3.8 nm
Dmax 13.0 nm
VolumePorod 110 nm3

SASDHC5 – Nuclear factor kB p50/RelA heterodimer

Transcription factor p65 19-549NF-kappa-B p105 subunit 39-350 experimental SAS data
BILBOMD model
Sample: Transcription factor p65 19-549 monomer, 58 kDa Mus musculus protein
NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 4.6 nm
Dmax 15.3 nm
VolumePorod 183 nm3

SASDHD5 – Transactivation domain of RelA

Transcription factor p65 340-549 experimental SAS data
MULTIFOXS model
Sample: Transcription factor p65 340-549 monomer, 23 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 2.7 nm
Dmax 8.2 nm
VolumePorod 59 nm3

SASDFF5 – Protein DPCD

Protein DPCD experimental SAS data
DAMMIF model
Sample: Protein DPCD monomer, 24 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Mar 21
Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol :167760 (2022)
Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X
RgGuinier 2.2 nm
Dmax 12.3 nm
VolumePorod 39 nm3