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- PDB-8oj1: Crystal structure of the DNA binding domain of M. polymorpha Auxi... -

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Basic information

Entry
Database: PDB / ID: 8oj1
TitleCrystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA
Components
  • Auxin response factor
  • HA7
KeywordsTRANSCRIPTION / Molecular caliper / Auxin Response Factor / 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
Auxin response factor domain / Auxin response factor / Auxin response factor ancillary 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 ...Auxin response factor domain / Auxin response factor / Auxin response factor ancillary 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.
Similarity search - Domain/homology
DNA / DNA (> 10) / Auxin response factor
Similarity search - Component
Biological speciesMarchantia polymorpha (common liverwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsCrespo, I. / Weijers, D. / Boer, D.R.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2020-117028 GB-I00 Spain
Ministry of Economy and Competitiveness (MINECO)BIO2016-77883-C2-2-P Spain
Ministry of Economy and Competitiveness (MINECO)FIS2015-72574-EXP Spain
CitationJournal: Structure / Year: 2025
Title: The structure and function of the DNA binding domain of class B MpARF2 share more traits with class A AtARF5 than to that of class B AtARF1.
Authors: Crespo, I. / Malfois, M. / Rienstra, J. / Tarres-Sole, A. / van den Berg, W. / Weijers, D. / Boer, D.R.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin response factor
B: HA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1783
Polymers47,1432
Non-polymers351
Water79344
1
A: Auxin response factor
B: HA7
hetero molecules

A: Auxin response factor
B: HA7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3566
Polymers94,2864
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area8250 Å2
ΔGint-73 kcal/mol
Surface area33310 Å2
Unit cell
Length a, b, c (Å)79.911, 80.933, 146.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11B-11-

DA

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Components

#1: Protein Auxin response factor


Mass: 40694.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marchantia polymorpha (common liverwort)
Gene: MARPO_0011s0167 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3FH20
#2: DNA chain HA7


Mass: 6448.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Marchantia polymorpha (common liverwort)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl, 20 mM DTT] and protein was added to final concentration of 5 mg/mL. Crystals of ...Details: Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl, 20 mM DTT] and protein was added to final concentration of 5 mg/mL. Crystals of MpARF2-DBD:DNA were obtained in 100 mM Tris pH 7-9, 18-33% PEG2KMME, 18.5% Glycerol by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). 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.
PH range: 7.0 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.566→70.86 Å / Num. obs: 15573 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 78.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.066 / Net I/σ(I): 20
Reflection shellResolution: 2.566→2.61 Å / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 42 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
PHASERphasing
Cootmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→70.86 Å / SU ML: 0.4082 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.3924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 756 4.86 %
Rwork0.2424 14813 -
obs0.2433 15569 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.74 Å2
Refinement stepCycle: LAST / Resolution: 2.57→70.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 448 1 44 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252797
X-RAY DIFFRACTIONf_angle_d0.53893903
X-RAY DIFFRACTIONf_chiral_restr0.039435
X-RAY DIFFRACTIONf_plane_restr0.0041426
X-RAY DIFFRACTIONf_dihedral_angle_d23.8244528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.760.41051470.3912902X-RAY DIFFRACTION99.74
2.76-3.040.40461860.34722892X-RAY DIFFRACTION99.94
3.04-3.480.31171230.30222965X-RAY DIFFRACTION99.97
3.48-4.390.2631290.22582989X-RAY DIFFRACTION99.78
4.39-70.860.21671710.20623065X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: -17.7518206805 Å / Origin y: 0.566878546012 Å / Origin z: -14.9441134602 Å
111213212223313233
T-2.19114988671 Å20.0180477428783 Å21.47756541758 Å2--0.622532387708 Å2-0.0776938970304 Å2---1.49088820976 Å2
L1.03929394994 °2-0.0203782727299 °20.125015396838 °2-0.224377579354 °20.185499183885 °2--2.53092277223 °2
S1.21537352056 Å °0.417312714575 Å °-1.4887460485 Å °0.16014361539 Å °0.860365387202 Å °0.629629142468 Å °3.08619303061 Å °-0.135802402807 Å °6.27640018126 Å °
Refinement TLS groupSelection details: all

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