Browse by MODEL: Ab initio only

SASDK64 – Signal recognition particle SRP9/14 heterodimer in complex with the 5' domain of SRP Alu RNA from Plasmodium falciparum

Signal recognition particle 9Signal recognition particle 14SRP Alu RNA 5' domain experimental SAS data
MONSA model
Sample: Signal recognition particle 9 monomer, 12 kDa Plasmodium falciparum protein
Signal recognition particle 14 monomer, 12 kDa Plasmodium falciparum protein
SRP Alu RNA 5' domain monomer, 24 kDa Plasmodium falciparum RNA
Buffer: 20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM MgCl2, 10 mM KCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 22
Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 4(1):600 (2021)
Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I
RgGuinier 3.2 nm
Dmax 11.9 nm
VolumePorod 77 nm3

SASDJS5 – Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial-monomer

Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial experimental SAS data
DAMMIN model
Sample: Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial monomer, 70 kDa Saccharomyces cerevisiae protein
Buffer: 40 mM Tris pH 7.5, 500 mM NaCl, 5% glycerol, 2.5 mM DTT, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 May 1
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae Acta Crystallographica Section D Structural Biology 77(6) (2021)
Alam J, Rahman F, Sah-Teli S, Venkatesan R, Koski M, Autio K, Hiltunen J, Kastaniotis A
RgGuinier 3.8 nm
Dmax 13.9 nm
VolumePorod 160 nm3

SASDJT5 – Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial-dimer

dimeric Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial experimental SAS data
DAMMIN model
Sample: Dimeric Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial dimer, 141 kDa Saccharomyces cerevisiae protein
Buffer: 40 mM Tris pH 7.5, 500 mM NaCl, 5% glycerol, 2.5 mM DTT, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 May 1
Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae Acta Crystallographica Section D Structural Biology 77(6) (2021)
Alam J, Rahman F, Sah-Teli S, Venkatesan R, Koski M, Autio K, Hiltunen J, Kastaniotis A
RgGuinier 5.0 nm
Dmax 18.2 nm
VolumePorod 516 nm3

SASDEC6 – Adenylation Domain of DNA ligase A with NAD+

DNA ligase A experimental SAS data
DAMMIF model
Sample: DNA ligase A monomer, 38 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Oct 6
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity Acta Crystallographica Section D Structural Biology 77(6) (2021)
Afsar M, Shukla A, Kumar N, Ramachandran R
RgGuinier 2.4 nm
Dmax 6.2 nm
VolumePorod 94 nm3

SASDG65 – Adenylation domain of DNA ligase A (LigA)

DNA ligase A experimental SAS data
GASBOR model
Sample: DNA ligase A monomer, 37 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 May 21
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity Acta Crystallographica Section D Structural Biology 77(6) (2021)
Afsar M, Shukla A, Kumar N, Ramachandran R
RgGuinier 2.7 nm
Dmax 8.9 nm
VolumePorod 68 nm3

SASDJU7 – HIV-1 Primer Binding Site (PBS)-Segment RNA

Primer Binding Site-Segment experimental SAS data
DAMMIF model
Sample: Primer Binding Site-Segment monomer, 33 kDa HIV-1: pNL4-3 RNA
Buffer: 10 mM Tris, 140 mM KCl, 10 mM NaCl, 1 mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Jul 29
The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res (2021)
Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X
RgGuinier 3.4 nm
Dmax 12.8 nm
VolumePorod 87 nm3

SASDKN8 – Rationally optimised WA20 (ROWA) tetramer

Rationally optimised WA20 mutant N22A/H86K (ROWA) tetramer experimental SAS data
DAMMIN model
Sample: Rationally optimised WA20 mutant N22A/H86K (ROWA) tetramer tetramer, 50 kDa Artificial protein (de … protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5% glycerol,, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2019 Nov 30
Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 11(1):7526 (2021)
Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R
RgGuinier 4.1 nm
Dmax 18.1 nm
VolumePorod 60 nm3

SASDKP8 – Rationally optimised WA20 (ROWA) hexamer

Rationally optimised WA20 mutant N22A/H86K (ROWA) hexamer experimental SAS data
DAMMIN model
Sample: Rationally optimised WA20 mutant N22A/H86K (ROWA) hexamer hexamer, 75 kDa Artificial protein (de … protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5% glycerol,, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2019 Nov 30
Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 11(1):7526 (2021)
Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R
RgGuinier 5.3 nm
Dmax 24.8 nm
VolumePorod 120 nm3

SASDKR8 – Rationally optimised SUWA (ROSA) tetramer

Rationally optimised SUWA mutant N22E/H86K (ROSA) tetramer experimental SAS data
DAMMIN model
Sample: Rationally optimised SUWA mutant N22E/H86K (ROSA) tetramer tetramer, 50 kDa Artificial protein (de … protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5% glycerol,, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2019 Nov 30
Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 11(1):7526 (2021)
Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R
RgGuinier 4.4 nm
Dmax 22.1 nm
VolumePorod 88 nm3

SASDXG3 – CP12 protein from the marine diatom Thalassiosira pseudonana

CP12 domain-containing protein experimental SAS data
GASBOR model
Sample: CP12 domain-containing protein dimer, 34 kDa Thalassiosira pseudonana protein
Buffer: 30 mM Tris, 50 mM NaCl, 2 mM EDTA, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Feb 23
A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana Cell Communication and Signaling 19(1) (2021)
Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H
RgGuinier 3.8 nm
Dmax 13.5 nm