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- PDB-7xp3: DNA complex form of ORESARA1(ANAC092) NAC Domain -

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Basic information

Entry
Database: PDB / ID: 7xp3
TitleDNA complex form of ORESARA1(ANAC092) NAC Domain
Components
  • DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
  • NAC domain-containing protein 92
KeywordsTRANSCRIPTION / Transcription factor / plant protein / TRANSCRIPTION regulator / DNA binding protein
Function / homology
Function and homology information


floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / response to ethylene / lateral root development / leaf senescence / regulation of seed germination / response to auxin / response to abscisic acid / response to salt ...floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / response to ethylene / lateral root development / leaf senescence / regulation of seed germination / response to auxin / response to abscisic acid / response to salt / positive regulation of programmed cell death / stress-induced premature senescence / positive regulation of DNA-binding transcription factor activity / response to salt stress / response to hydrogen peroxide / regulation of gene expression / response to oxidative stress / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / NAC domain-containing protein 92
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Plant Commun. / Year: 2023
Title: Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.
Authors: Chun, I. / Kim, H.J. / Hong, S. / Kim, Y.G. / Kim, M.S.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: The crystal structure of ORE1(ANAC092) NAC domain in complex with DNA
Authors: Chun, I.S.
History
DepositionMay 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92
C: NAC domain-containing protein 92
E: DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')
G: DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)76,5977
Polymers76,5977
Non-polymers00
Water00
1
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92
E: DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,1054
Polymers51,1054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NAC domain-containing protein 92
G: DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')
H: DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)25,4923
Polymers25,4923
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.592, 92.592, 216.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11G-12-

DG

21G-12-

DG

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Components

#1: Protein NAC domain-containing protein 92 / ANAC092 / AtNAC2 / AtNAC6 / Protein ORESARA 1


Mass: 18800.699 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NAC92, NAC2, NAC6, ORE1, At5g39610, MIJ24.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FKA0
#2: DNA chain DNA (5'-D(*AP*GP*TP*TP*AP*CP*GP*TP*AP*CP*GP*GP*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 6745.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*CP*CP*GP*TP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 6758.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#4: DNA chain DNA (5'-D(P*GP*TP*TP*AP*CP*GP*TP*GP*TP*GP*C)-3')


Mass: 3693.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: half of occupancy nucleotide / Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#5: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*GP*TP*AP*AP*C)-3')


Mass: 2997.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)

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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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium sulfate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.24→46.3 Å / Num. obs: 16649 / % possible obs: 99.49 % / Redundancy: 17 % / CC1/2: 0.947 / Net I/σ(I): 18.4
Reflection shellResolution: 3.245→3.361 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 1663 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data collection
PHENIX1.17.1_3660phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XLJ

7xlj


Resolution: 3.25→46.3 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 832 5.04 %
Rwork0.2131 --
obs0.215 16504 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 1463 0 0 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0265236
X-RAY DIFFRACTIONf_angle_d1.5417391
X-RAY DIFFRACTIONf_dihedral_angle_d24.9962016
X-RAY DIFFRACTIONf_chiral_restr0.104785
X-RAY DIFFRACTIONf_plane_restr0.013682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.450.34581370.29022564X-RAY DIFFRACTION98
3.45-3.720.34661360.29512627X-RAY DIFFRACTION100
3.72-4.090.28651370.25292602X-RAY DIFFRACTION100
4.09-4.690.24471390.21222615X-RAY DIFFRACTION100
4.69-5.90.27111400.22012622X-RAY DIFFRACTION100
5.9-46.30.21511430.18032642X-RAY DIFFRACTION99
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)
10.4403-0.2749-0.31460.1641-0.07280.3203-1.27-0.7102-1.55630.65140.21661.54131.35240.8354-01.0735-0.03880.06581.6317-0.02111.3779-34.2498-27.194242.9854
23.05790.3394-1.89190.59080.97183.4309-0.02980.043-0.0682-0.3121-0.47450.42-0.6663-0.696300.76980.0188-0.10921.3744-0.21640.9333-31.3024-24.506825.7999
32.0108-3.0886-0.34115.80131.19510.4477-2.3696-1.63090.61072.57960.97174.34790.0094-4.5598-0.37231.5619-0.0952-0.14222.498-0.28931.8684-38.1078-17.790134.5553
41.05930.3230.21612.2643-0.94530.22810.1593-0.05330.5097-0.16540.20021.3337-0.8545-1.1307-00.97170.066-0.00881.3625-0.09690.9257-26.2066-13.368119.2743
50.19681.05970.04412.95890.2460.71111.0196-0.542-1.3482-1.8723-1.0463-1.32760.11251.1128-0.03390.8524-0.068-0.08731.3405-0.0670.8936-13.2924-23.604331.0713
61.68360.29561.31912.7878-0.68421.43180.20120.7066-0.1988-0.5815-0.2778-0.3519-0.8905-0.355600.9597-0.03430.00581.2327-0.13740.6608-23.0026-17.476925.2
70.4753-0.70850.67011.98090.30280.9801-1.2383-0.1971-0.83020.43771.14770.74190.8826-0.411301.1979-0.042-0.15411.97020.07261.0762-33.9175-24.63351.6716
81.97735.09592.01552.7592.15843.31881.9952-3.2362-5.47710.3922.38021.36590.966-3.13132.98681.51080.27650.82152.21560.37531.9994-35.0558-30.642662.8193
91.2862-0.24390.33320.1336-0.66832.589-1.5791-1.0393-1.939-1.65432.3804-3.72412.5642-0.22630.12411.9416-0.111-0.24711.173-0.20592.1104-17.2771-33.316862.8898
101.2754-1.6487-0.28341.82780.34110.02120.42530.4684-1.3467-0.5531-0.70470.6271-0.1775-0.9822-01.2688-0.0297-0.15041.4987-0.55692.0119-24.3496-30.339655.824
110.33740.7269-0.46741.57830.09660.77420.3507-0.52440.1168-0.03210.0482-0.6166-0.5865-0.3781-01.3220.0384-0.06191.57320.10321.3517-15.457-22.003370.91
120.14690.4582-0.63611.4554-2.22663.92542.1645-1.41780.9876-2.57680.72970.2231-2.6595-1.47360.68811.9699-0.3373-0.17361.5077-0.3641.7037-27.8708-9.666256.7091
132.32041.61732.14223.46640.68181.3553-0.2917-0.0347-0.69620.47820.13570.42790.21110.0551-00.99430.0370.0671.1797-0.13911.3144-17.4131-19.877560.532
140.19990.32770.04551.6623-0.65680.5345-0.7202-0.88691.8637-1.64462.79920.3011-0.8080.83470.01252.26540.6050.89921.8457-0.04441.7959-35.3987-18.307373.767
150.9411.14220.14861.3282-0.01540.47062.0409-0.07960.99460.75450.4583-0.9165-0.1077-0.44910.00231.06230.0907-0.00191.7379-0.20421.2299-23.0848-24.77958.1262
163.0689-2.38482.89823.85860.0853.02840.50660.4945-0.617-1.80910.212-1.22121.16050.3915-02.0333-0.2870.3041.3345-0.2461.1362-35.05527.520768.5827
170.7989-0.94610.08891.16630.05280.0502-1.09490.81410.0698-0.08440.90832.7842-2.1122-1.354-0.06731.8-0.2152-0.64231.44430.06071.0704-44.803518.038972.9288
180.2913-0.24520.50540.1242-0.26940.5817-1.95622.43981.3089-1.92181.18471.3433-0.6532-0.189201.8528-0.4151-0.22111.4383-0.38841.8854-31.591115.29374.7051
191.97611.05610.47730.6434-0.42411.7542-0.0877-0.25680.62320.4230.28890.05560.1188-0.827701.1422-0.1839-0.15660.69950.01561.2539-28.883320.232285.0843
203.15171.02720.86510.50970.82881.58740.4321-3.006-1.1561-1.43251.8534-1.91093.32913.23940.2032.34880.4376-0.11521.4623-0.44411.659-28.1257-0.574882.638
213.481.43231.60430.48580.65183.4271.0181.45241.83740.2353-1.7697-1.86040.8962-1.1426-0.31291.2848-0.2588-0.17120.536-0.10351.4962-37.052417.477688.1689
221.4092-0.55451.59611.4341-1.49872.1540.2198-0.7190.5333-0.52970.8659-0.2161.0551-0.60530.00011.2131-0.36740.04320.7395-0.16391.4295-34.409910.390678.1916
230.49510.54470.7030.19460.61060.71290.25281.07720.59390.18860.12160.1405-1.58871.0101.8368-0.1672-0.00071.59740.05151.1512-14.2884-4.751922.3053
240.79590.29441.2402-0.02250.45310.8929-0.54090.11940.01240.64880.8244-0.0157-2.22550.3352-01.7192-0.1557-0.04911.6112-0.10961.1576-10.4349-9.747758.1721
250.64660.03630.023-0.0546-0.0276-0.0364-0.81321.0851-1.5381-0.74711.1886-0.2386-1.61891.75901.8018-0.1103-0.15841.6309-0.06051.2501-8.3493-17.952473.3816
260.3284-0.8698-0.48181.14350.78561.270.36290.46360.00070.6520.946-0.2537-0.05960.7675-01.7545-0.2062-0.34631.8002-0.14341.5203-11.0753-8.853149.5944
270.8662-0.53250.20870.1969-0.02390.08890.72111.56770.3664-0.71820.008-0.7733-0.8915-0.87502.1221-0.333-0.02731.5667-0.14571.4128-12.824-2.372622.1974
280.9664-0.76570.38160.4045-0.2478-0.2640.4037-1.11880.20010.5435-1.14430.2430.9581-0.556-0.00232.0406-0.5452-0.00221.2035-0.09011.7787-33.771212.887896.2455
290.41390.41560.6996-0.0770.09730.46021.6417-2.1013-1.45931.6348-1.6773-1.81711.1302-1.0254-0.02011.9293-0.6975-0.2761.33420.14882.1069-33.914710.241195.0733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 114 )
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 103 )
12X-RAY DIFFRACTION12chain 'B' and (resid 104 through 115 )
13X-RAY DIFFRACTION13chain 'B' and (resid 116 through 148 )
14X-RAY DIFFRACTION14chain 'B' and (resid 149 through 160 )
15X-RAY DIFFRACTION15chain 'B' and (resid 161 through 170 )
16X-RAY DIFFRACTION16chain 'C' and (resid 19 through 61 )
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 75 )
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 85 )
19X-RAY DIFFRACTION19chain 'C' and (resid 87 through 104 )
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 118 )
21X-RAY DIFFRACTION21chain 'C' and (resid 119 through 137 )
22X-RAY DIFFRACTION22chain 'C' and (resid 138 through 170 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 10 )
24X-RAY DIFFRACTION24chain 'E' and (resid 11 through 22 )
25X-RAY DIFFRACTION25chain 'F' and (resid 23 through 27 )
26X-RAY DIFFRACTION26chain 'F' and (resid 28 through 37 )
27X-RAY DIFFRACTION27chain 'F' and (resid 38 through 44 )
28X-RAY DIFFRACTION28chain 'G' and (resid 1 through 12 )
29X-RAY DIFFRACTION29chain 'H' and (resid 35 through 44 )

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