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- PDB-8cra: Structure of the keratin-like domain of SEPALLATA3 and AGAMOUS fr... -

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Basic information

Entry
Database: PDB / ID: 8cra
TitleStructure of the keratin-like domain of SEPALLATA3 and AGAMOUS from Arabidopsis thaliana
Components
  • Developmental protein SEPALLATA 3Development of the human body
  • Floral homeotic protein AGAMOUS
KeywordsPLANT PROTEIN / MADS transcription factor / floral organ development / carpel development / tetramerization domain / heterotetramer
Function / homology
Function and homology information


specification of floral organ number / mucilage extrusion from seed coat / specification of floral organ identity / seed coat development / plant ovule development / flower development / cell fate specification / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell differentiation / protein dimerization activity ...specification of floral organ number / mucilage extrusion from seed coat / specification of floral organ identity / seed coat development / plant ovule development / flower development / cell fate specification / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor, K-box / K-box region / K-box domain profile. / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS
Similarity search - Domain/homology
Developmental protein SEPALLATA 3 / Floral homeotic protein AGAMOUS
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZubieta, C. / Hugouvieux, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Structure of the keratin-like domain of SEPALLATA3 and AGAMOUS from Arabidopsis thaliana
Authors: Zubieta, C. / Hugouvieux, V.
History
DepositionMar 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Floral homeotic protein AGAMOUS
B: Floral homeotic protein AGAMOUS
C: Floral homeotic protein AGAMOUS
D: Floral homeotic protein AGAMOUS
E: Developmental protein SEPALLATA 3
F: Developmental protein SEPALLATA 3
G: Developmental protein SEPALLATA 3
H: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)91,0078
Polymers91,0078
Non-polymers00
Water2,072115
1
A: Floral homeotic protein AGAMOUS
B: Floral homeotic protein AGAMOUS
E: Developmental protein SEPALLATA 3
H: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)45,5044
Polymers45,5044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-79 kcal/mol
Surface area23440 Å2
MethodPISA
2
C: Floral homeotic protein AGAMOUS
D: Floral homeotic protein AGAMOUS
F: Developmental protein SEPALLATA 3
G: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)45,5044
Polymers45,5044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-83 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.335, 138.372, 180.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Floral homeotic protein AGAMOUS


Mass: 11307.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AG, At4g18960, F13C5.130 / Production host: Escherichia coli (E. coli) / References: UniProt: P17839
#2: Protein
Developmental protein SEPALLATA 3 / Development of the human body / Agamous-like MADS-box protein AGL9


Mass: 11443.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SEP3, AGL9, At1g24260, F3I6.19 / Production host: Escherichia coli (E. coli) / References: UniProt: O22456
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, pH 8.0, 2M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→82 Å / Num. obs: 95018 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rrim(I) all: 0.097 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.45 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6627 / CC1/2: 0.347 / Rrim(I) all: 1.63 / % possible all: 0.932

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.399 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27911 2417 4.9 %RANDOM
Rwork0.23669 ---
obs0.2388 46989 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.085 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.56 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 0 115 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126094
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166115
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.6518147
X-RAY DIFFRACTIONr_angle_other_deg0.4651.57214021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3245728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.516574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.926101310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4035.6962939
X-RAY DIFFRACTIONr_mcbond_other4.4015.6962939
X-RAY DIFFRACTIONr_mcangle_it6.58410.213658
X-RAY DIFFRACTIONr_mcangle_other6.58410.213659
X-RAY DIFFRACTIONr_scbond_it5.5786.3293155
X-RAY DIFFRACTIONr_scbond_other5.5776.3293156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.71111.4054490
X-RAY DIFFRACTIONr_long_range_B_refined10.99857.166882
X-RAY DIFFRACTIONr_long_range_B_other10.98857.176869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 178 -
Rwork0.348 3267 -
obs--95.43 %
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)
10.74910.32040.27280.20110.03930.19650.0695-0.03150.12730.078-0.02020.1405-0.05770.0163-0.04940.3362-0.09690.03640.0621-0.00280.143751.889741.1164176.6956
22.93970.37010.86790.27070.0520.27170.09470.234-0.12160.258-0.02730.0409-0.03720.0771-0.06740.2986-0.01280.11820.07980.05260.157520.868541.2408152.2904
30.15790.1017-0.06710.1765-0.08910.1854-0.1260.0462-0.0659-0.11470.14920.03450.08130.0489-0.02320.236-0.0575-0.03650.17120.01470.188339.0505-7.5317158.6184
41.05270.5372-0.15521.2302-0.31440.12450.16620.3311-0.082-0.0951-0.02510.13320.00880.0038-0.14110.2611-0.0571-0.09240.2603-0.02960.187833.981221.8126132.8922
50.858-0.18070.34490.0765-0.15960.67780.0512-0.0388-0.25330.04330.08110.062-0.2102-0.0873-0.13240.2463-0.0515-0.08180.11260.08050.152142.234322.9695172.7162
60.3185-0.1485-0.33971.2768-0.64570.9636-0.04370.0098-0.02580.05640.14070.1364-0.0107-0.031-0.0970.182-0.0833-0.03220.0999-0.02130.09446.483311.6253160.8005
70.16950.7501-0.3884.2146-0.8371.81170.12990.03580.13960.31250.00550.8888-0.3498-0.3215-0.13550.2179-0.0397-0.10360.12690.10230.377820.49725.3225138.649
82.92220.09580.7910.06620.30941.6783-0.13660.47440.31110.03060.03210.0164-0.02860.11210.10450.1503-0.00730.02380.12970.09830.135136.276551.4443152.2351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 192
2X-RAY DIFFRACTION2B97 - 187
3X-RAY DIFFRACTION3C99 - 190
4X-RAY DIFFRACTION4D99 - 191
5X-RAY DIFFRACTION5E80 - 175
6X-RAY DIFFRACTION6F83 - 175
7X-RAY DIFFRACTION7G88 - 175
8X-RAY DIFFRACTION8H88 - 175

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