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- PDB-6sdg: Crystal structure of the DNA binding domain of M. polymorpha Auxi... -

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Basic information

Entry
Database: PDB / ID: 6sdg
TitleCrystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA
Components
  • 21-7_A
  • 21-7_B
  • Auxin response factor
KeywordsTRANSCRIPTION / Transcription Factor / DNA binding / Nucleus / Hormone Response
Function / homology
Function and homology information


auxin-activated signaling pathway / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain ...SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / PB1 domain profile. / PB1 domain / SH3 type barrels. / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Auxin response factor / Auxin response factor
Similarity search - Component
Biological speciesMarchantia polymorpha (liverwort)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsCrespo, I. / Weijers, D. / Boer, D.R.
Citation
Journal: Nat.Plants / Year: 2020
Title: Design principles of a minimal auxin response system.
Authors: Kato, H. / Mutte, S.K. / Suzuki, H. / Crespo, I. / Das, S. / Radoeva, T. / Fontana, M. / Yoshitake, Y. / Hainiwa, E. / van den Berg, W. / Lindhoud, S. / Ishizaki, K. / Hohlbein, J. / Borst, ...Authors: Kato, H. / Mutte, S.K. / Suzuki, H. / Crespo, I. / Das, S. / Radoeva, T. / Fontana, M. / Yoshitake, Y. / Hainiwa, E. / van den Berg, W. / Lindhoud, S. / Ishizaki, K. / Hohlbein, J. / Borst, J.W. / Boer, D.R. / Nishihama, R. / Kohchi, T. / Weijers, D.
#1: Journal: Nat.Plants / Year: 2020
Title: Design principles of a minimal auxin response system
Authors: Kato, H. / Mutte, S.K. / Suzuki, H. / Crespo, I. / Das, S. / Radoeva, T. / Fontana, M. / Yoshitake, Y. / Hainiwa, E. / van den Berg, W. / Lindhoud, S. / Hohlbein, J. / Borst, J.W. / Boer, D. ...Authors: Kato, H. / Mutte, S.K. / Suzuki, H. / Crespo, I. / Das, S. / Radoeva, T. / Fontana, M. / Yoshitake, Y. / Hainiwa, E. / van den Berg, W. / Lindhoud, S. / Hohlbein, J. / Borst, J.W. / Boer, D.R. / Nishihama, R. / Kohchi, T. / Ishizak, K. / Weijers, D.
History
DepositionJul 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxin response factor
B: Auxin response factor
C: 21-7_A
D: 21-7_B


Theoretical massNumber of molelcules
Total (without water)94,2774
Polymers94,2774
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Different DNAs tested and peak mobility checked against calibration curve. Retention time fits the corresponding for a complex between 21-7 dsDNA and a dimer of MpARF2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-60 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.768, 79.360, 79.767
Angle α, β, γ (deg.)90.000, 116.929, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEGLNGLN(chain 'A' and (resid 24 through 63 or resid 69...AA24 - 6324 - 63
121ILEILEGLNGLN(chain 'A' and (resid 24 through 63 or resid 69...AA69 - 10869 - 108
131SERSERARGARG(chain 'A' and (resid 24 through 63 or resid 69...AA126 - 232126 - 232
141LYSLYSSERSER(chain 'A' and (resid 24 through 63 or resid 69...AA239 - 304239 - 304
151PROPROASNASN(chain 'A' and (resid 24 through 63 or resid 69...AA307 - 360307 - 360
261ILEILEGLNGLN(chain 'B' and (resid 24 through 232 or resid 239 through 360))BB24 - 6324 - 63
271ILEILEGLNGLN(chain 'B' and (resid 24 through 232 or resid 239 through 360))BB69 - 10869 - 108
281SERSERARGARG(chain 'B' and (resid 24 through 232 or resid 239 through 360))BB126 - 232126 - 232
291LYSLYSSERSER(chain 'B' and (resid 24 through 232 or resid 239 through 360))BB239 - 304239 - 304
2101PROPROASNASN(chain 'B' and (resid 24 through 232 or resid 239 through 360))BB307 - 360307 - 360
1112DTDTDGDG(chain 'C' and (resid 0 through 8 or resid 12 through 20))CC0 - 81 - 9
1122DCDCDADA(chain 'C' and (resid 0 through 8 or resid 12 through 20))CC12 - 2013 - 21
2132DTDTDGDG(chain 'D' and (resid 0 through 8 or resid 12 through 20))DD0 - 81 - 9
2142DCDCDADA(chain 'D' and (resid 0 through 8 or resid 12 through 20))DD12 - 2013 - 21

NCS ensembles :
ID
1
2

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Components

#1: Protein Auxin response factor


Mass: 40694.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marchantia polymorpha (liverwort) / Gene: MpARF2 / Plasmid: pTWIN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: A0A0K2QVG1, UniProt: A0A0G3FH20*PLUS
#2: DNA chain 21-7_A


Mass: 6439.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain 21-7_B


Mass: 6448.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 % / Description: Cube-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl] and protein was added to final concentration of 5 mg/mL. Crystals of MpARF2-DBD:DNA ...Details: Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl] and protein was added to final concentration of 5 mg/mL. Crystals of MpARF2-DBD:DNA were obtained in 0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350 by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). Cube-shaped crystals appeared in less than a week. Cryo-cooling in liquid nitrogen was carried out using a cryo-protecting solution containing reservoir solution supplemented with 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationMonochromator: Channel cut Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.96→29.2 Å / Num. obs: 14035 / % possible obs: 73.52 % / Redundancy: 3.3 % / Biso Wilson estimate: 101.11 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/av σ(I): 1.11 / Net I/σ(I): 8.2
Reflection shellResolution: 2.96→3.423 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.641 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1336 / % possible all: 5.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDX

4ldx


Resolution: 2.96→29.2 Å / SU ML: 0.4858 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.3336
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2775 768 5.48 %
Rwork0.2149 13246 -
obs0.2183 14014 73.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.71 Å2
Refinement stepCycle: LAST / Resolution: 2.96→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 896 0 0 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01326128
X-RAY DIFFRACTIONf_angle_d1.45068509
X-RAY DIFFRACTIONf_chiral_restr0.075924
X-RAY DIFFRACTIONf_plane_restr0.0093957
X-RAY DIFFRACTIONf_dihedral_angle_d19.99173548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.190.4793360.3918743X-RAY DIFFRACTION20.63
3.19-3.510.37651290.3122006X-RAY DIFFRACTION56.41
3.51-4.010.34721950.2713280X-RAY DIFFRACTION91.4
4.01-5.050.27111970.20893587X-RAY DIFFRACTION99.27
5.05-29.20.24172110.18113630X-RAY DIFFRACTION98.74
Refinement TLS params.Method: refined / Origin x: 32.106204392 Å / Origin y: 56.7470847469 Å / Origin z: 16.8740073752 Å
111213212223313233
T0.689626566759 Å20.058445062087 Å2-0.0116795328676 Å2-0.349253719147 Å20.0233729434469 Å2--0.482766010149 Å2
L2.46040428184 °2-0.265043951266 °20.480848197131 °2-0.738043378499 °20.0862746575827 °2--0.431717435798 °2
S-0.300193589597 Å °-0.427818301695 Å °-0.225306433161 Å °0.15783592539 Å °0.211933781248 Å °0.0584168478184 Å °-0.239283306345 Å °-0.123980001732 Å °0.110438039813 Å °
Refinement TLS groupSelection details: all

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