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- PDB-9lpe: ATPDF2 HDZIP domain complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 9lpe
TitleATPDF2 HDZIP domain complexed with DNA
Components
  • DNA (5'-D(*CP*TP*AP*AP*AP*TP*GP*CP*AP*GP*TP*GP*CP*AP*TP*TP*TP*A)-3')
  • DNA (5'-D(*GP*TP*AP*AP*AP*TP*GP*CP*AP*CP*TP*GP*CP*AP*TP*TP*TP*A)-3')
  • Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
KeywordsDNA BINDING PROTEIN/DNA / HD-ZIP transcription factors / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


maintenance of floral organ identity / cotyledon development / regulation of seed dormancy process / regulation of seed germination / seed germination / epidermal cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity ...maintenance of floral organ identity / cotyledon development / regulation of seed dormancy process / regulation of seed germination / seed germination / epidermal cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / lipid binding / DNA binding / nucleus
Similarity search - Function
Homeobox-leucine zipper protein GLABRA2/ANL2/PDF2/ATML1-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Homeobox-leucine zipper protein GLABRA2/ANL2/PDF2/ATML1-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / START-like domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsChen, W. / Huang, H.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC Grant No. 31930096 and 1902034 China
CitationJournal: Plant Physiol. / Year: 2025
Title: Molecular insights into DNA recognition by HD-Zip transcription factors.
Authors: Chen, W. / Yan, W. / Jiang, K. / Huang, H.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
B: Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
C: DNA (5'-D(*CP*TP*AP*AP*AP*TP*GP*CP*AP*GP*TP*GP*CP*AP*TP*TP*TP*A)-3')
D: DNA (5'-D(*GP*TP*AP*AP*AP*TP*GP*CP*AP*CP*TP*GP*CP*AP*TP*TP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)37,9494
Polymers37,9494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-16 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.278, 73.278, 170.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Homeobox-leucine zipper protein PROTODERMAL FACTOR 2


Mass: 13459.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93V99
#2: DNA chain DNA (5'-D(*CP*TP*AP*AP*AP*TP*GP*CP*AP*GP*TP*GP*CP*AP*TP*TP*TP*A)-3')


Mass: 5514.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*GP*TP*AP*AP*AP*TP*GP*CP*AP*CP*TP*GP*CP*AP*TP*TP*TP*A)-3')


Mass: 5514.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES monohydrate PH 6.0, 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 9792 / % possible obs: 97 % / Redundancy: 3.6 % / Biso Wilson estimate: 62.53 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.115 / Net I/σ(I): 3.5
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.225 / Num. unique obs: 935 / CC1/2: 0.973 / CC star: 0.993 / Rpim(I) all: 0.145 / Rrim(I) all: 0.27 / Χ2: 0.292

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→35.82 Å / Cross valid method: FREE R-VALUE / σ(F): 249.24 / Phase error: 35.42 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2824 465 4.75 %
Rwork0.2742 --
obs0.276 9792 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 732 0 0 1897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112172
X-RAY DIFFRACTIONf_angle_d1.1853095
X-RAY DIFFRACTIONf_dihedral_angle_d25.796825
X-RAY DIFFRACTIONf_chiral_restr0.055337
X-RAY DIFFRACTIONf_plane_restr0.01291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.560.28691420.28922997X-RAY DIFFRACTION91
3.56-4.480.281560.28563060X-RAY DIFFRACTION92
4.48-35.820.28541520.26513285X-RAY DIFFRACTION94
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)
12.36821.3251-0.76872.8104-0.32691.13250.03570.44270.4244-0.35180.25390.2161-0.3303-0.1972-0.14681.2138-0.6310.40550.2704-0.15530.853326.3013-4.0427-5.7823
22.14710.5964-0.43333.245-0.15071.5705-0.02080.22470.0453-0.27590.0428-0.2452-0.07780.1946-0.05190.5466-0.9644-0.07380.1628-0.14250.558831.8764-11.4622-5.2642
34.6680.8946-0.23626.086-2.15481.8950.1696-0.40370.27420.45610.3594-0.0018-0.99480.421-0.54450.9515-0.10520.23961.3175-0.1380.529527.6827-30.7658-2.4007
46.43372.2124-0.58776.8661-2.43233.6753-0.02950.2954-0.9241-0.65050.2168-1.5262-0.39170.8313-0.17120.7245-0.17450.09051.4422-0.20080.667938.1462-40.2884-8.7239
54.29721.2511-1.26694.662-2.61072.8606-0.19610.9386-0.5592-1.41520.5581-0.6933-0.12230.454-0.36040.8969-0.27280.20821.3237-0.28960.668330.419-41.2307-16.226
64.01940.4172-0.19025.869-1.86172.9107-0.17880.63460.3298-0.66030.1392-1.9641-0.88671.20990.00551.1703-0.34890.37671.651-0.26980.909345.765-24.954-14.2741
72.9733-0.75870.69292.4008-0.49750.2079-0.0138-0.05690.12140.22920.1637-0.4124-0.24220.3688-0.11540.8972-0.8603-0.03770.5107-0.5230.170128.2307-18.0423-9.3052
80.85380.2888-0.08751.01080.52221.563-0.4368-0.47670.01380.57640.5575-0.5313-0.41790.4895-0.1271.3064-0.2541-0.06291.076-0.40660.518237.4017-22.07176.7629
91.13210.4940.48210.99661.00371.1548-0.225-0.33360.09550.30690.4178-0.4926-0.04720.1645-0.24441.98050.103-0.34151.6527-0.0813-0.07536.229-13.25425.7019
100.71330.25140.3660.4781.07692.5048-0.08260.0695-0.12450.5790.1915-0.24380.7172-0.40440.0111.80250.3783-0.39771.1805-0.16820.262542.0865-14.293834.2039
110.12190.26950.35260.58520.77761.0382-0.1861-0.2491-0.11840.5360.09380.10120.3934-0.52350.10351.65220.1529-0.16651.6819-0.22790.330732.408-16.543718.9173
120.62090.36090.01711.25961.50022.1127-0.3863-0.0595-0.01430.39590.239-0.2045-0.0629-0.16840.08041.1704-0.1849-0.03221.2165-0.08950.400738.7845-16.44831.0104
130.5866-0.28790.58331.2880.92981.8669-0.1952-0.1856-0.08530.54270.08380.10180.0932-0.3190.06970.906-0.28560.30921.0892-0.5193-0.088530.4874-26.9412-7.9048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 117 )
3X-RAY DIFFRACTION3chain 'B' and (resid 66 through 70 )
4X-RAY DIFFRACTION4chain 'B' and (resid 71 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 102 )
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 137 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 10 )
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 18 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 10 )
12X-RAY DIFFRACTION12chain 'D' and (resid 11 through 15 )
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 18 )

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