Browse by MODEL: Ab initio only

SASDFH7 – Pseudomonas putida CBB5 NdmAB complex

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 127 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 129 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 May 21
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 4.2 nm
Dmax 10.9 nm

SASDFJ7 – Pseudomonas putida CBB5 mCherry-NdmA/ECFP-NdmB complex - static

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 207 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 208 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at 4C, Pohang Accelerator Laboratory on 2018 Jul 27
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 5.6 nm
Dmax 19.1 nm

SASDDA6 – Class I chitinase 2 from Agave tequilana

Chitinase 2 experimental SAS data
DAMMIF model
Sample: Chitinase 2 monomer, 32 kDa Agave tequilana protein
Buffer: MES 50 mM, pH: 6
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2017 Apr 19
A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins. FEBS J (2019)
Sierra-Gómez Y, Rodríguez-Hernández A, Cano-Sánchez P, Gómez-Velasco H, Hernández-Santoyo A, Siliqi D, Rodríguez-Romero A
RgGuinier 2.4 nm
Dmax 9.8 nm
VolumePorod 49 nm3

SASDDE7 – Class I chitinase 1 from Agave tequilana

Chitinase 1 experimental SAS data
DAMMIF model
Sample: Chitinase 1 monomer, 32 kDa Agave tequilana protein
Buffer: MES 50 mM, pH: 6
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2017 Apr 26
A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins. FEBS J (2019)
Sierra-Gómez Y, Rodríguez-Hernández A, Cano-Sánchez P, Gómez-Velasco H, Hernández-Santoyo A, Siliqi D, Rodríguez-Romero A
RgGuinier 2.6 nm
Dmax 9.7 nm
VolumePorod 52 nm3

SASDEF9 – TraI of Neisseria gonorrhoeae

TraI experimental SAS data
GASBOR model
Sample: TraI monomer, 91 kDa Neisseria gonorrhoeae protein
Buffer: 50 mM TRIS-HCl 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2018 Mar 5
DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island. Nucleic Acids Res 47(15):8136-8153 (2019)
Heilers JH, Reiners J, Heller EM, Golzer A, Smits SHJ, van der Does C
RgGuinier 7.3 nm
Dmax 31.4 nm
VolumePorod 293 nm3

SASDFS3 – Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D

Transcription intermediary factor 1-beta experimental SAS data
GASBOR model
Sample: Transcription intermediary factor 1-beta dimer, 82 kDa Mus musculus protein
Buffer: 10 mM Tris 300 mM NaCl 0.1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Aug 10
A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol (2019)
Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC
RgGuinier 7.0 nm
Dmax 23.2 nm
VolumePorod 232 nm3

SASDFT3 – Murine transcription intermediary factor 1-beta, TRIM28 RBCC assembly-null mutation R184D, complexed with the Krab domain of ZFP809 fused to an N-terminal MBP

Transcription intermediary factor 1-betaZinc finger protein 809 N-terminal MBP fusion experimental SAS data
GASBOR model
Sample: Transcription intermediary factor 1-beta dimer, 82 kDa Mus musculus protein
Zinc finger protein 809 N-terminal MBP fusion monomer, 52 kDa Mus musculus protein
Buffer: 10 mM Tris 300 mM NaCl 0.1 mM TCEP, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Aug 10
A Dissection of Oligomerisation by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol (2019)
Sun Y, Keown JR, Black MM, Raclot C, Demarais N, Trono D, Turelli P, Goldstone DC
RgGuinier 6.4 nm
Dmax 22.0 nm
VolumePorod 252 nm3

SASDF72 – roX2 RNA stem-loop 7 18mer-fragment

roX2 stem-loop 7, 18-mer fragment experimental SAS data
DAMMIN model
Sample: RoX2 stem-loop 7, 18-mer fragment monomer, 12 kDa synthetic construct RNA
Buffer: 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 29
Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Nucleic Acids Res 47(8):4319-4333 (2019)
Ankush Jagtap PK, Müller M, Masiewicz P, von Bülow S, Hollmann NM, Chen PC, Simon B, Thomae AW, Becker PB, Hennig J
RgGuinier 1.8 nm
Dmax 8.5 nm
VolumePorod 14 nm3

SASDF82 – Urokinase plasminogen activator surface receptor, uPAR H47C-N259C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).

Urokinase plasminogen activator surface receptorUrokinase-type plasminogen activator (Amino Terminal Fragment) experimental SAS data
DAMMIN model
Sample: Urokinase plasminogen activator surface receptor monomer, 37 kDa Homo sapiens protein
Urokinase-type plasminogen activator (Amino Terminal Fragment) monomer, 16 kDa Homo sapiens protein
Buffer: 20 mM PBS, 5 %(v/v) glycerol, 50 mM NaSO4,, pH: 7.4
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 18
Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond? J Biol Chem (2019)
Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M
RgGuinier 2.6 nm
Dmax 8.2 nm
VolumePorod 102 nm3

SASDF92 – Urokinase plasminogen activator surface receptor, uPAR, T51C-V70C

Urokinase plasminogen activator surface receptor experimental SAS data
DAMMIN model
Sample: Urokinase plasminogen activator surface receptor monomer, 37 kDa Homo sapiens protein
Buffer: 20 mM PBS, 5 %(v/v) glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Dec 1
Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond? J Biol Chem (2019)
Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M
RgGuinier 2.5 nm
Dmax 8.9 nm
VolumePorod 55 nm3