Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.

Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M
Nat Commun 11(1):2905 (2020 Jun 9)

PMID: 32518228
doi: 10.1038/s41467-020-16724-5

Submitted to SASBDB: 2019 Apr 26
Published in SASBDB: 2020 Apr 21

SASDFR6 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (ratio DNA:Protein 1:1)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 228 kDa Escherichia coli protein
Buffer:	20mM HEPES, 100mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jul 8

R_g^Guinier	6.1	nm
D_max	21.9	nm
Volume^Porod	251	nm³

SASDFS6 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (ratio DNA:Protein 1:2.5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 267 kDa Escherichia coli protein
Buffer:	20mM HEPES, 100mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jul 8

R_g^Guinier	7.0	nm
D_max	25.0	nm
Volume^Porod	386	nm³

SASDFT6 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (ratio DNA:Protein 1:5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 267 kDa Escherichia coli protein
Buffer:	20mM HEPES, 100mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jul 8

R_g^Guinier	7.2	nm
D_max	27.0	nm
Volume^Porod	474	nm³

SASDFU6 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (ratio DNA:Protein 1:10)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 305 kDa Escherichia coli protein
Buffer:	20mM HEPES, 100mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jul 8

R_g^Guinier	8.0	nm
D_max	24.8	nm
Volume^Porod	448	nm³

SASDFN6 – DNA-binding protein HU-alpha

DNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	DNA-binding protein HU-alpha octamer, 77 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

R_g^Guinier	3.2	nm
D_max	10.7	nm

SASDFP6 – 80 base pair DNA

80bp_DNA Forward80bp_DNA Reverse experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	7.0	nm
D_max	28.9	nm

SASDF36 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 4.5 with 50 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM sodium acetate, 50 mM NaCl, pH: 4.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

SASDF46 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 4.5 with 100 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM sodium acetate, 100 mM NaCl, pH: 4.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

SASDF56 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 4.5 with 150 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM sodium acetate, 150 mM NaCl, pH: 4.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

SASDF66 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 4.5 with 300 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM sodium acetate, 300 mM NaCl, pH: 4.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

SASDFX5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 5.5 with 50 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 50 mM NaCl, pH: 5.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

SASDFY5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 5.5 with 100 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 5.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

SASDFZ5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 5.5 with 150 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 150 mM NaCl, pH: 5.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

SASDF26 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 5.5 with 300 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha decamer, 95 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 300 mM NaCl, pH: 5.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

R_g^Guinier	6.4	nm
D_max	24.4	nm
Volume^Porod	268	nm³

SASDFT5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 6.5 with 50 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, 10 kDa Escherichia coli protein
Buffer:	10mM Bis-Tris, 50 mM NaCl, pH: 6.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

SASDFU5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 6.5 with 100 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha 14-mer, 133 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 6.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	6.2	nm
D_max	24.4	nm
Volume^Porod	274	nm³

SASDFV5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 6.5 with 150 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha 14-mer, 133 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 150 mM NaCl, pH: 6.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	7.0	nm
D_max	26.2	nm
Volume^Porod	352	nm³

SASDFW5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 6.5 with 300 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha decamer, 95 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 300 mM NaCl, pH: 6.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	6.0	nm
D_max	24.7	nm
Volume^Porod	218	nm³

SASDFP5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 7.5 with 50 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha 16-mer, 153 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 50 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 27

R_g^Guinier	8.9	nm
D_max	28.5	nm
Volume^Porod	410	nm³

SASDFQ5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 7.5 with 100 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha 16-mer, 153 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	6.6	nm
D_max	25.0	nm
Volume^Porod	336	nm³

SASDFR5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 7.5 with 150 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha 14-mer, 133 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 150 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	5.8	nm
D_max	24.2	nm
Volume^Porod	308	nm³

SASDFS5 – DNA-binding protein HU-alpha bound to 80 base-pair DNA at pH 7.5 with 300 mM NaCl

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha experimental SAS data

CHIMERA model

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha decamer, 95 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 300 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	6.5	nm
D_max	24.0	nm
Volume^Porod	242	nm³

SASDFQ6 – DNA-binding protein HU-alpha, E34K

DNA-binding protein HU-alpha, E34K experimental SAS data

CHIMERA model

Sample:	DNA-binding protein HU-alpha, E34K dimer, 19 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 100 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 1

R_g^Guinier	2.2	nm
D_max	6.7	nm
Volume^Porod	36	nm³

SASDGB3 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (pH 4.5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha, E34K Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K dimer, 19 kDa Escherichia coli protein
Buffer:	10 mM sodium acetate, 50 mM NaCl, pH: 4.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 2

SASDGC3 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (pH 5.5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha, E34K Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K dimer, 19 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 50 mM NaCl, pH: 5.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 2

SASDGD3 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (pH 6.5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha, E34K Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 100 kDa Escherichia coli protein
Buffer:	10mM Bis-Tris, 50 mM NaCl, pH: 6.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 2

R_g^Guinier	7.3	nm
D_max	28.0	nm
Volume^Porod	330	nm³

SASDGE3 – DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (pH 7.5)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data

80bp_DNA Forward 80bp_DNA Reverse DNA-binding protein HU-alpha, E34K Kratky plot

Sample:	80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA 80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA DNA-binding protein HU-alpha, E34K, 100 kDa Escherichia coli protein
Buffer:	10 mM Bis-Tris, 50 mM NaCl, pH: 7.5
Experiment:	SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Nov 2

R_g^Guinier	7.1	nm
D_max	27.5	nm
Volume^Porod	309	nm³