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- PDB-6ycq: Crystal structure of the DNA binding domain of Arabidopsis thalia... -

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Basic information

Entry
Database: PDB / ID: 6ycq
TitleCrystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA
Components
  • 21-7A
  • 21-7B
  • Auxin response factor 1
KeywordsTRANSCRIPTION / Transcription Factor / DNA binding / Nucleus / Hormone Response
Function / homology
Function and homology information


leaf senescence / response to auxin / cell death / auxin-activated signaling pathway / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Auxin response factor domain / Auxin response factor / Auxin response factor / 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 / 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
Similarity search - Domain/homology
FORMIC ACID / DNA / DNA (> 10) / Auxin response factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCrespo, I. / Weijers, D. / Boer, D.R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-77883-C2-2-P Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis .
Authors: Freire-Rios, A. / Tanaka, K. / Crespo, I. / van der Wijk, E. / Sizentsova, Y. / Levitsky, V. / Lindhoud, S. / Fontana, M. / Hohlbein, J. / Boer, D.R. / Mironova, V. / Weijers, D.
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxin response factor 1
B: Auxin response factor 1
C: 21-7A
D: 21-7B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09125
Polymers95,0464
Non-polymers1,04521
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-171 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.304, 102.784, 127.039
Angle α, β, γ (deg.)90.000, 98.036, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Auxin response factor 1


Mass: 41079.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARF1, At1g59750, F23H11.7 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L7G0

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 21-7A


Mass: 6430.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain 21-7B


Mass: 6457.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 5 types, 669 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: B10 condition of the Morpheus HT screen: 0.09 M (0.3M Sodium fluoride, 0.3M Sodium bromide, 0.3M Sodium iodide); 0.1 M (Tris (base), BICINE pH8.5); 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→47.58 Å / Num. obs: 75146 / % possible obs: 88.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.97 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.9
Reflection shellResolution: 1.651→1.68 Å / Num. unique obs: 82 / CC1/2: 0.512

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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: 1.65→47.57 Å / SU ML: 0.1762 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.094
RfactorNum. reflection% reflection
Rfree0.1991 3634 4.84 %
Rwork0.1717 --
obs0.173 75141 57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 855 52 648 7081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796746
X-RAY DIFFRACTIONf_angle_d0.96349328
X-RAY DIFFRACTIONf_chiral_restr0.05521003
X-RAY DIFFRACTIONf_plane_restr0.00571069
X-RAY DIFFRACTIONf_dihedral_angle_d14.04945258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.265150.264447X-RAY DIFFRACTION1.06
1.67-1.70.30240.2784108X-RAY DIFFRACTION2.27
1.7-1.720.3537150.3116193X-RAY DIFFRACTION4.11
1.72-1.750.3837180.3116316X-RAY DIFFRACTION6.6
1.75-1.770.342180.2846411X-RAY DIFFRACTION8.64
1.77-1.80.3505250.2839526X-RAY DIFFRACTION10.76
1.8-1.830.2843400.2821752X-RAY DIFFRACTION15.86
1.83-1.870.3279580.2602913X-RAY DIFFRACTION19.26
1.87-1.90.3098510.28161215X-RAY DIFFRACTION25.01
1.9-1.940.2943850.25861522X-RAY DIFFRACTION31.69
1.94-1.980.2593970.24311860X-RAY DIFFRACTION38.8
1.98-2.030.27571350.23792432X-RAY DIFFRACTION50.97
2.03-2.080.27841080.24512412X-RAY DIFFRACTION49.61
2.08-2.140.25621960.2244147X-RAY DIFFRACTION86.2
2.14-2.20.24282400.21274499X-RAY DIFFRACTION93.53
2.2-2.270.24911340.22393029X-RAY DIFFRACTION61.9
2.27-2.350.26092520.20664664X-RAY DIFFRACTION97.89
2.35-2.450.22962260.19814708X-RAY DIFFRACTION97.05
2.45-2.560.21372290.20154748X-RAY DIFFRACTION97.63
2.56-2.690.22472310.19494764X-RAY DIFFRACTION98.72
2.69-2.860.2142590.19064745X-RAY DIFFRACTION98.33
2.86-3.080.20242350.17654711X-RAY DIFFRACTION97.77
3.08-3.390.18052670.15714702X-RAY DIFFRACTION97.72
3.39-3.880.17372280.14614543X-RAY DIFFRACTION93.48
3.88-4.890.14352360.12464743X-RAY DIFFRACTION97.34
4.89-47.570.18192420.14514797X-RAY DIFFRACTION97.18
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4287516539450.0217316809332-0.1897542918813.117641025260.02387336726540.302428607704-0.00795072891494-0.165787149157-0.04824205611810.02656333324380.0175358574945-0.152894532476-0.01619054659610.00566607248665-0.02603161438790.131308945607-0.000260130542432-0.0209332978160.196143547321-0.002842461436550.1414634670753.968416587141.7029122059450.8148909733
21.704280674230.122552209616-0.6022350263690.9719615766931.227978139082.29539247010.02911822950570.120785443635-0.0679066312823-0.182037940112-0.2538050215160.05922234224130.017176907599-0.1411257766120.1956933217790.1638296854350.0118293946973-0.0063337725790.211301955018-0.03286735628110.2242973985781.63831103375-13.959954746336.3981713804
34.60633976309-0.177501999052-0.7010548571960.724196631997-0.3500715351311.244845188380.021847282509-0.07758729599560.07210443371680.01410056406420.06891398097510.124896121256-0.0264156232385-0.130101690351-0.1067506427120.147384525164-0.00750003205937-0.0109017788780.1577435554790.0218687983770.156791221667-12.6091691409-13.831286016251.0924633816
42.742249135540.139392535904-0.07748763105793.888250371780.4569935173162.41696559926-0.0794930183910.0670888225359-0.078152373810.04994887829450.0631999239520.160751745318-0.1188627653870.08195054201270.007516594378360.09637060769-0.02407499213640.008690074376270.145221936704-0.03098761898580.1454066773229.96606627589-16.088759475818.7346436154
50.4860114402640.164109124773-0.3464039177712.74430770268-0.6754237480050.7430501586980.01701498960880.1795162890070.0249597338351-0.1281041722330.1538885420030.150006778649-0.0810490227596-0.137796097872-0.1759475731290.152214596497-0.0253831988279-0.01634838995070.2633802451320.03504456908810.212022650168.881028353022.8363054960512.0263895048
65.42269980386-0.169840450998-0.5801245322280.8008420463980.6030428705210.939169254548-0.008365059929140.16292919262-0.0298479784833-0.02142417366390.0484449405284-0.06971793216160.005063744806180.0533994754123-0.03762359109780.153696619897-0.0108766138817-0.01605537784320.176074515861-0.0339849139430.14313117416425.5023657038-18.13473069315.3955191183
73.83367407186-1.31163121223-2.409058965622.239666376860.6448787830442.817271687280.334452802604-0.2629211678180.4965060775910.5136026109350.0278339271119-0.449338160361-1.136492707930.00833652159337-0.3983541515640.603473791778-0.02261059174620.12422992750.316875746461-0.006958273712470.38894142293417.150521521428.650407787114.1164525627
81.00622049822-0.689106176382-1.435059794021.018865127650.05094437380075.032003927160.1468287656780.3500839035750.31174696312-0.5378385479660.0247183017911-0.0271167738826-0.348565164664-0.602834312192-0.1101356788030.4428842134320.06736938715530.03937367702280.294631818180.004830630469770.238355715221-2.1628493137731.458336875341.5086388957
94.920653367410.963302978069-2.328463246354.561584059870.00944396735753.896026127120.1417958998820.6033147087790.707544617009-0.7424999162170.2044196184990.142719178336-0.835806140472-0.399804188854-0.3284744612920.4103205629080.06594297565390.005748173286240.2669073483110.0008519108515130.258951718065-3.1102355730431.868015425742.3215938083
101.712177196011.502188317130.3620177619351.86039326044-1.146300095925.65191325174-0.114849328670.05770124684770.1329969888590.3485186535830.10703560456-0.373144871821-0.576886217039-0.1560275227540.07463936784490.551921349350.03489724221080.1465695633470.2120843487750.01126557194210.40912483875316.050848697928.417794706515.0912023791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 223 )
2X-RAY DIFFRACTION2chain 'A' and (resid 224 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 355 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 99 )
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 256 )
6X-RAY DIFFRACTION6chain 'B' and (resid 257 through 355 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 21 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 10 )
10X-RAY DIFFRACTION10chain 'D' and (resid 11 through 21 )

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