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25 hits found for Klumpler

SASDC62 – Basic domain of telomeric repeat-binding factor 2 (TRF2)

Basic domain of telomeric repeat-binding factor 2 experimental SAS data
Basic domain of telomeric repeat-binding factor 2 Kratky plot
Sample: Basic domain of telomeric repeat-binding factor 2 monomer, 5 kDa Homo sapiens protein
Buffer: 50 mM NaPi, 50 mM NaCl, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2015 Mar 5
Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
...Klumpler T, Hofr C
RgGuinier 1.7 nm
Dmax 7.1 nm
VolumePorod 4 nm3

SASDCZ2 – Yeast CTDsome: transcription termination factor Rtt103p/C-terminal domain of DNA-directed RNA polymerase II subunit RPB1 (Rtt103 1-246-phospho-mimetic complex)

Regulator of Ty1 transposition protein 103DNA-directed RNA polymerase II subunit RPB1 experimental SAS data
CORAL model
Sample: Regulator of Ty1 transposition protein 103 dimer, 57 kDa Saccharomyces cerevisiae protein
DNA-directed RNA polymerase II subunit RPB1 monomer, 13 kDa Saccharomyces cerevisiae protein
Buffer: 25 mM KH2PO4, 300 mM KCl, 10 mM BME, pH: 6.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 Apr 12
Structure and dynamics of the RNAPII CTDsome with Rtt103. Proc Natl Acad Sci U S A 114(42):11133-11138 (2017)
...Klumpler T, Kubicek K, Kalynych S, Plevka P, Stefl R
RgGuinier 5.3 nm
Dmax 21.0 nm
VolumePorod 561 nm3

SASDD73 – Flavin reductase Pden_5119

NADPH-dependent FMN reductase experimental SAS data
SWISSMODEL model
Sample: NADPH-dependent FMN reductase dimer, 41 kDa Paracoccus denitrificans protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 Feb 22
Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans. Int J Mol Sci 24(4) (2023)
Kryl M, Sedláček V, Kučera I
RgGuinier 2.3 nm
Dmax 6.3 nm
VolumePorod 70 nm3

SASDDN6 – Human stress-inducible heat shock 70 kDa protein 1, Hsp70 (Hspa1a) T204A mutant dimer, in the presence of ATP

Heat shock 70 kDa protein 1 experimental SAS data
MODELLER model
Sample: Heat shock 70 kDa protein 1 dimer, 147 kDa Homo sapiens protein
Buffer: 50mM HEPES, 150mM KCH3COO, 2mM MgCl2, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2018 Feb 20
Human stress-inducible Hsp70 has a high propensity to form ATP-dependent antiparallel dimers that are differentially regulated by co-chaperone binding. Mol Cell Proteomics (2018)
...Klumpler T, Vojtesek B, Muller P, Man P
RgGuinier 4.0 nm
Dmax 11.6 nm
VolumePorod 248 nm3

SASDTK7 – RECQ like helicase 5 (1 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Mar 29
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 6.5 nm
Dmax 19.5 nm
VolumePorod 310 nm3

SASDTL7 – RECQ like helicase 5 (4 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Mar 29
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 6.4 nm
Dmax 20.2 nm
VolumePorod 288 nm3

SASDTM7 – RECQ like helicase 5 fragment (amino acids 625-825; 0.2 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 21 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Apr 19
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 3.7 nm
Dmax 9.3 nm
VolumePorod 73 nm3

SASDTN7 – RECQ like helicase 5 fragment (amino acids 625-825; 0.4 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Apr 19
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 3.9 nm
Dmax 10.1 nm
VolumePorod 91 nm3

SASDHP7 – Haloalkane dehalogenase variant DhaA115 - monomeric fraction

Haloalkane dehalogenase variant DhaA115 -monomeric fraction experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Haloalkane dehalogenase variant DhaA115 -monomeric fraction monomer, 34 kDa Rhodococcus rhodochrous protein
Buffer: 50 mM potassium phosphate buffer (41 mM K₂HPO₄, 9mM KH₂PO₄), pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2019 Aug 22
Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst Chemical Science 11(41):11162-11178 (2020)
Markova K, Chmelova K, Marques S, Carpentier P, Bednar D, Damborsky J, Marek M
RgGuinier 1.9 nm
Dmax 6.0 nm
VolumePorod 41 nm3

SASDTP7 – RECQ like helicase 5 fragment (amino acids 625-825; 0.6 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Apr 19
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 4.3 nm
Dmax 11.2 nm
VolumePorod 116 nm3

SASDHQ7 – Haloalkane dehalogenase variant DhaA115 - dimeric fraction

Haloalkane dehalogenase variant DhaA115 - dimeric fraction experimental SAS data
CORAL model
Sample: Haloalkane dehalogenase variant DhaA115 - dimeric fraction dimer, 69 kDa Rhodococcus rhodochrous protein
Buffer: 50 mM potassium phosphate buffer (41 mM K₂HPO₄, 9mM KH₂PO₄), pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2019 Aug 22
Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst Chemical Science 11(41):11162-11178 (2020)
Markova K, Chmelova K, Marques S, Carpentier P, Bednar D, Damborsky J, Marek M
RgGuinier 2.9 nm
Dmax 8.9 nm
VolumePorod 78 nm3

SASDTQ7 – RECQ like helicase 5 fragment (amino acids 625-825; 0.8 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Apr 19
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 4.6 nm
Dmax 13.2 nm
VolumePorod 102 nm3

SASDTR7 – RECQ like helicase 5 fragment (amino acids 625-825; 1.0 mg/ml)

ATP-dependent DNA helicase Q5 experimental SAS data
ATP-dependent DNA helicase Q5 Kratky plot
Sample: ATP-dependent DNA helicase Q5 , 109 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 200 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2023 Apr 19
Mechanisms of transcription attenuation and condensation of RNA polymerase II by RECQ5
Tomas Klumpler
RgGuinier 5.7 nm
Dmax 16.2 nm
VolumePorod 150 nm3

SASDF29 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4ADP-ribosylation factor1 - short experimental SAS data
OTHER model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 monomer, 8 kDa Homo sapiens protein
ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2015 Dec 10
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
...Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 21 nm3

SASDF39 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

ADP-ribosylation factor1 - shortDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 experimental SAS data
OTHER model
Sample: ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2018 May 29
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
...Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.1 nm
Dmax 6.4 nm
VolumePorod 39 nm3

SASDF49 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 - long

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4ADP-ribosylation factor1 - long experimental SAS data
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 ADP-ribosylation factor1 - long Kratky plot
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
ADP-ribosylation factor1 - long monomer, 16 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Sep 20
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
...Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.5 nm
Dmax 7.0 nm
VolumePorod 53 nm3

SASDB79 – Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex

Basic domain of telomeric repeat-binding factor 2telomere DNA duplex experimental SAS data
MONSA model
Sample: Basic domain of telomeric repeat-binding factor 2 monomer, 5 kDa Homo sapiens protein
telomere DNA duplex monomer, 11 kDa DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
...Klumpler T, Hofr C
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 20 nm3

SASDB89 – Telomeric DNA duplex

telomere DNA duplex experimental SAS data
MONSA model
Sample: telomere DNA duplex monomer, 11 kDa DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
...Klumpler T, Hofr C
RgGuinier 1.6 nm
Dmax 5.7 nm
VolumePorod 12 nm3

SASDWG9 – PDZ domain of the segment polarity protein dishevelled homolog DVL-3

Segment polarity protein dishevelled homolog DVL-3 experimental SAS data
REFMAC model
Sample: Segment polarity protein dishevelled homolog DVL-3 monomer, 12 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA, pH: 6.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2021 Jan 27
A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain. Structure (2025)
...Klumpler T, Bystrý V, Sprangers R, Bařinka C, Bryja V, Tripsianes K
RgGuinier 1.6 nm
Dmax 4.3 nm
VolumePorod 20 nm3

SASDSQ9 – NanoLuc luciferase

Oplophorus-luciferin 2-monooxygenase catalytic subunit experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Oplophorus-luciferin 2-monooxygenase catalytic subunit monomer, 20 kDa Oplophorus gracilirostris protein
Buffer: 10 mM Tris-HCl, 50 mM NaCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2021 May 27
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun 14(1):7864 (2023)
Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M
RgGuinier 1.8 nm
Dmax 5.9 nm
VolumePorod 38 nm3

SASDL32 – Transcription elongation factor SPT6

Transcription elongation factor SPT6 experimental SAS data
Transcription elongation factor SPT6 Rg histogram
Sample: Transcription elongation factor SPT6 monomer, 145 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 25 mM NaPi; 150mM NaCl; 0.5 mM EDTA; 5% glycerol; 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Oct 22
Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res (2022)
...Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R
RgGuinier 4.5 nm
Dmax 12.0 nm
VolumePorod 249 nm3

SASDUU5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 bound to 3'UTR fragment of ADP-ribosylation factor 1

Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177)3'UTR fragment of ADP-ribosylation factor 1 experimental SAS data
CORAL model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 (Δ1-177) dimer, 89 kDa Homo sapiens protein
3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2020 May 4
A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy. Curr Protoc 5(1):e70084 (2025)
Tripepi A, Shakoor H, Klapetek P
RgGuinier 4.9 nm
Dmax 13.4 nm
VolumePorod 129 nm3

SASDL22 – Transcription elongation factor SPT6 - ΔtSH2 variant

Transcription elongation factor SPT6 - ΔtSH2 variant experimental SAS data
Transcription elongation factor SPT6 - ΔtSH2 variant Rg histogram
Sample: Transcription elongation factor SPT6 - ΔtSH2 variant monomer, 122 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 25 mM NaPi; 150mM NaCl; 0.5 mM EDTA; 5% glycerol; 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Oct 22
Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res (2022)
...Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R
RgGuinier 4.1 nm
Dmax 13.9 nm
VolumePorod 245 nm3

SASDKZ9 – Transcription elongation factor SPT6 - ΔN Spt6

Transcription elongation factor SPT6 - ΔN Spt6 variant experimental SAS data
Transcription elongation factor SPT6 - ΔN Spt6 Rg histogram
Sample: Transcription elongation factor SPT6 - ΔN Spt6 variant monomer, 132 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 25 mM Hepes; 150 NaCl; 0.5 mM EDTA; 5% glycerol; 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Oct 3
Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res (2022)
...Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R
RgGuinier 4.7 nm
Dmax 14.4 nm
VolumePorod 288 nm3

SASDUV5 – Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to 3'UTR fragment of ADP-ribosylation factor 1

3'UTR fragment of ADP-ribosylation factor 1Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) experimental SAS data
CORAL model
Sample: 3'UTR fragment of ADP-ribosylation factor 1 monomer, 14 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) dimer, 81 kDa Homo sapiens protein
Buffer: 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH: 7
Experiment: SAXS data collected at Rigaku BioSAXS-2000, CEITEC on 2024 Jan 12
A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy. Curr Protoc 5(1):e70084 (2025)
Tripepi A, Shakoor H, Klapetek P
RgGuinier 5.5 nm
Dmax 16.1 nm
VolumePorod 139 nm3