Browse by MODEL: Ab initio only

SASDDN9 – Mycobacterium tuberculosis DNA Ligase A

DNA ligase A experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 5.2 nm
Dmax 16.7 nm
VolumePorod 870 nm3

SASDDV9 – Mycobacterium tuberculosis DNA LigaseA with Nicked DNA

DNA ligase ANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Nicked DNA dimer, 16 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 4.4 nm
Dmax 14.8 nm
VolumePorod 262 nm3

SASDEW3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA)

DNA ligase AProbable exodeoxyribonuclease III protein XthA experimental SAS data
DAMMIF model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 6.2 nm
Dmax 23.9 nm
VolumePorod 662 nm3

SASDEX3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA

DNA ligase AProbable exodeoxyribonuclease III protein XthANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
Nicked DNA monomer, 8 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res (2020)
Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R
RgGuinier 4.5 nm
Dmax 17.1 nm
VolumePorod 117 nm3

SASDHS5 – Full-length Mouse TIFA dimer

TRAF-interacting protein with FHA domain-containing protein A experimental SAS data
DAMFILT model
Sample: TRAF-interacting protein with FHA domain-containing protein A dimer, 45 kDa Mus musculus protein
Buffer: 20 mM HEPES, 150 mM NaCl, 100 mM arginine, 5 % glycerol, 10 mM DTT, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, Kumamoto University on 2014 Oct 16
Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity. Sci Rep 10(1):5152 (2020)
Nakamura T, Hashikawa C, Okabe K, Yokote Y, Chirifu M, Toma-Fukai S, Nakamura N, Matsuo M, Kamikariya M, Okamoto Y, Gohda J, Akiyama T, Semba K, Ikemizu S, Otsuka M, Inoue JI, Yamagata Y
RgGuinier 3.1 nm
Dmax 15.5 nm
VolumePorod 85 nm3

SASDHC2 – PieE-FAD: 2,4-dichlorophenol 6-monooxygenase bound to flavin adenine dinucleotide

2,4-dichlorophenol 6-monooxygenaseFlavin adenine dinucleotide experimental SAS data
DAMMIN model
Sample: 2,4-dichlorophenol 6-monooxygenase hexamer, 399 kDa Streptomyces sp. SCSIO … protein
Flavin adenine dinucleotide hexamer, 5 kDa
Buffer: 20 mM Tris, 150 mM NaCl, 5 mM DTT, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at Xenocs BioXolver L with MetalJet, Département de Biochimie, Université de Montréal on 2019 Oct 22
Structural analyses of the group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem (2020)
Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R
RgGuinier 4.8 nm
Dmax 13.2 nm
VolumePorod 624 nm3

SASDH45 – Histone Deacetylase 1 (HDAC1) and Lysine-specific Demethylase 1 (LSD1) in the complex with CoREST

Histone deacetylase 1Lysine-specific histone demethylase 1AREST corepressor 1 experimental SAS data
DAMFILT model
Sample: Histone deacetylase 1 monomer, 55 kDa Homo sapiens protein
Lysine-specific histone demethylase 1A monomer, 93 kDa Homo sapiens protein
REST corepressor 1 monomer, 46 kDa Homo sapiens protein
Buffer: 25 mM Tris/Cl, 50 mM potassium acetate and 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2015 Jan 23
Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex. Cell Rep 30(8):2699-2711.e8 (2020)
Song Y, Dagil L, Fairall L, Robertson N, Wu M, Ragan TJ, Savva CG, Saleh A, Morone N, Kunze MBA, Jamieson AG, Cole PA, Hansen DF, Schwabe JWR
RgGuinier 6.0 nm
Dmax 15.8 nm
VolumePorod 437 nm3

SASDGC6 – Glucuronoyl esterase, deglycolsylated full length

4-O-methyl-glucuronoyl methylesterase (Glucuronoyl esterase) experimental SAS data
DAMMIN model
Sample: 4-O-methyl-glucuronoyl methylesterase (Glucuronoyl esterase) monomer, 51 kDa Cerrena unicolor protein
Buffer: 20 mM sodium acetate, pH: 5
Experiment: SAXS data collected at Xenocs BioXolver L with GeniX3D, University of Copenhagen, Department of Drug Design and Pharmacology on 2018 Oct 10
The structural basis of fungal glucuronoyl esterase activity on natural substrates. Nat Commun 11(1):1026 (2020)
Ernst HA, Mosbech C, Langkilde AE, Westh P, Meyer AS, Agger JW, Larsen S
RgGuinier 3.2 nm
Dmax 11.0 nm
VolumePorod 71 nm3

SASDHM3 – Human Telomerase Reverse Transcriptase Core Promoter G-rich Region (hTERT_WT) DNA

Human Telomerase Reverse Transcriptase Core Promoter G-rich Region experimental SAS data
DAMMIF model
Sample: Human Telomerase Reverse Transcriptase Core Promoter G-rich Region monomer, 22 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2018 Oct 5
The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res (2020)
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, Chaires JB, Trent JO
RgGuinier 2.2 nm
Dmax 8.1 nm
VolumePorod 28 nm3

SASDHN3 – Antiparallel Hairpin (AH) DNA

Antiparallel Hairpin experimental SAS data
DAMMIF model
Sample: Antiparallel Hairpin monomer, 21 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Nov 3
The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res (2020)
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, Chaires JB, Trent JO
RgGuinier 2.5 nm
Dmax 8.1 nm
VolumePorod 28 nm3