Browse by MODEL: Hybrid

SASDJZ4 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer )

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
DsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 6.5 nm
Dmax 23.1 nm
VolumePorod 1090 nm3

SASDJ25 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer/dimer)

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
DsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 7.5 nm
Dmax 29.4 nm
VolumePorod 1440 nm3

SASDJR3 – BceAB-type ABC-Transporter nucleotide-binding domain, SaNsrF

ABC transporter, ATP-binding protein (Nucleotide-Binding Domain SaNsrF) experimental SAS data
OTHER model
Sample: ABC transporter, ATP-binding protein (Nucleotide-Binding Domain SaNsrF) monomer, 31 kDa Streptococcus agalactiae protein
Buffer: 100 mM HEPES, 150 mM NaCl, 10% glycerol, pH: 8
Experiment: SAXS data collected at Xenocs Xeuss 2.0 Q-Xoom, Center for Structural Studies, Heinrich-Heine-University on 2019 Dec 11
Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae Scientific Reports 10(1) (2020)
Furtmann F, Porta N, Hoang D, Reiners J, Schumacher J, Gottstein J, Gohlke H, Smits S
RgGuinier 2.4 nm
Dmax 7.9 nm
VolumePorod 64 nm3

SASDH59 – Human Cation-independent mannose-6-phosphate receptor domains 9-10 wih mannose-6-phosphate

Cation-independent mannose-6-phosphate receptor experimental SAS data
OTHER model
Sample: Cation-independent mannose-6-phosphate receptor dimer, 67 kDa Homo sapiens protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Jan 25
Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7–11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9 Structure (2020)
Bochel A, Williams C, McCoy A, Hoppe H, Winter A, Nicholls R, Harlos K, Jones E, Berger I, Hassan A, Crump M
RgGuinier 3.3 nm
Dmax 9.1 nm
VolumePorod 88 nm3

SASDH69 – Human Cation-independent mannose-6-phosphate receptor domains 9-10: Deglycosylated

Cation-independent mannose-6-phosphate receptor experimental SAS data
OTHER model
Sample: Cation-independent mannose-6-phosphate receptor monomer, 34 kDa Homo sapiens protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Mar 3
Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7–11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9 Structure (2020)
Bochel A, Williams C, McCoy A, Hoppe H, Winter A, Nicholls R, Harlos K, Jones E, Berger I, Hassan A, Crump M
RgGuinier 2.5 nm
Dmax 7.8 nm
VolumePorod 48 nm3

SASDH79 – Human Cation-independent mannose-6-phosphate receptor domains 9-10

Cation-independent mannose-6-phosphate receptor experimental SAS data
MULTIFOXS model
Sample: Cation-independent mannose-6-phosphate receptor dimer, 67 kDa Homo sapiens protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Jan 25
Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7–11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9 Structure (2020)
Bochel A, Williams C, McCoy A, Hoppe H, Winter A, Nicholls R, Harlos K, Jones E, Berger I, Hassan A, Crump M
RgGuinier 3.3 nm
Dmax 9.2 nm
VolumePorod 93 nm3

SASDJ23 – Human Cation-independent mannose-6-phosphate receptor domains 9-10: Deglycosylated with mannose-6-phosphate

Cation-independent mannose-6-phosphate receptor experimental SAS data
MULTIFOXS model
Sample: Cation-independent mannose-6-phosphate receptor monomer, 34 kDa Homo sapiens protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Mar 3
Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7–11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9 Structure (2020)
Bochel A, Williams C, McCoy A, Hoppe H, Winter A, Nicholls R, Harlos K, Jones E, Berger I, Hassan A, Crump M
RgGuinier 2.5 nm
Dmax 7.8 nm
VolumePorod 69 nm3

SASDKT9 – The Moco-free form of the Moco carrier protein from Rippkaea orientalis

p450 cytochrome, putative (Moco carrier protein) experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: P450 cytochrome, putative (Moco carrier protein) tetramer, 75 kDa Rippkaea orientalis (strain … protein
Buffer: 100 mM Tris-HCl, 300 mM NaCl, 2 %(v/v) glycerol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2015 Feb 5
The structure of the Moco carrier protein from Rippkaea orientalis. Acta Crystallogr F Struct Biol Commun 76(Pt 9):453-463 (2020)
Krausze J, Hercher TW, Archna A, Kruse T
RgGuinier 2.8 nm
Dmax 8.5 nm
VolumePorod 107 nm3

SASDFT8 – The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element HoxB13 DR0

Retinoic acid receptor alpha, RARRetinoic acid receptor RXR-alphaDNA response element HoxB13 DR0 experimental SAS data
CORAL model
Sample: Retinoic acid receptor alpha, RAR monomer, 41 kDa Mus musculus protein
Retinoic acid receptor RXR-alpha monomer, 38 kDa Mus musculus protein
DNA response element HoxB13 DR0 monomer, 10 kDa DNA
Buffer: 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 19
Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR Nucleic Acids Research (2020)
Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N
RgGuinier 3.8 nm
Dmax 14.5 nm
VolumePorod 132 nm3

SASDFU8 – The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element F11r DR5.

Retinoic acid receptor alpha, RARRetinoic acid receptor RXR-alphaDNA response element F11r DR5 experimental SAS data
CORAL model
Sample: Retinoic acid receptor alpha, RAR monomer, 41 kDa Mus musculus protein
Retinoic acid receptor RXR-alpha monomer, 38 kDa Mus musculus protein
DNA response element F11r DR5 monomer, 13 kDa DNA
Buffer: 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 19
Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR Nucleic Acids Research (2020)
Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 130 nm3