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- PDB-7nb0: Structure of the DNA-binding domain of SEPALLATA 3 -

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Basic information

Entry
Database: PDB / ID: 7nb0
TitleStructure of the DNA-binding domain of SEPALLATA 3
ComponentsDevelopmental protein SEPALLATA 3Development of the human body
KeywordsPLANT PROTEIN / Transcription factor / MADS family / DNA-binding domain
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 / protein dimerization activity / DNA-binding transcription factor 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 / protein dimerization activity / DNA-binding transcription factor activity / 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
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZubieta, C. / Nanao, M.H.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE92-0023 France
Grenoble Instruct-ERIC Center (ISBG)13317 France
CitationJournal: Nat Commun / Year: 2021
Title: The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors.
Authors: Lai, X. / Vega-Leon, R. / Hugouvieux, V. / Blanc-Mathieu, R. / van der Wal, F. / Lucas, J. / Silva, C.S. / Jourdain, A. / Muino, J.M. / Nanao, M.H. / Immink, R. / Kaufmann, K. / Parcy, F. / ...Authors: Lai, X. / Vega-Leon, R. / Hugouvieux, V. / Blanc-Mathieu, R. / van der Wal, F. / Lucas, J. / Silva, C.S. / Jourdain, A. / Muino, J.M. / Nanao, M.H. / Immink, R. / Kaufmann, K. / Parcy, F. / Smaczniak, C. / Zubieta, C.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Developmental protein SEPALLATA 3
B: Developmental protein SEPALLATA 3
C: Developmental protein SEPALLATA 3
D: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)26,4154
Polymers26,4154
Non-polymers00
Water1,18966
1
A: Developmental protein SEPALLATA 3
C: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)13,2072
Polymers13,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area6800 Å2
MethodPISA
2
B: Developmental protein SEPALLATA 3
D: Developmental protein SEPALLATA 3


Theoretical massNumber of molelcules
Total (without water)13,2072
Polymers13,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-24 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.404, 67.436, 122.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-120-

HOH

21B-115-

HOH

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Components

#1: Protein
Developmental protein SEPALLATA 3 / Development of the human body / Agamous-like MADS-box protein AGL9


Mass: 6603.718 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: potassium sodium tartrate tetrahydrate (0.2M), bis-tris propane (0.1M, pH 7.5) and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 16555 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.084 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 1188 / CC1/2: 0.564 / Rrim(I) all: 1.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KOV

3kov


Resolution: 2.1→47.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.161 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 1651 10 %RANDOM
Rwork0.20351 ---
obs0.20683 14874 98.97 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.465 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å20 Å2
2--0.42 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 66 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191834
X-RAY DIFFRACTIONr_bond_other_d0.0010.021804
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9272445
X-RAY DIFFRACTIONr_angle_other_deg1.0482.9384160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37422.09981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5781520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_mcbond_it2.5373.326894
X-RAY DIFFRACTIONr_mcbond_other2.523.324893
X-RAY DIFFRACTIONr_mcangle_it3.7164.9651113
X-RAY DIFFRACTIONr_mcangle_other3.7154.9661114
X-RAY DIFFRACTIONr_scbond_it3.0933.669938
X-RAY DIFFRACTIONr_scbond_other3.0933.669938
X-RAY DIFFRACTIONr_scangle_other4.7775.3611333
X-RAY DIFFRACTIONr_long_range_B_refined7.00338.1842062
X-RAY DIFFRACTIONr_long_range_B_other6.9538.0952057
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 115 -
Rwork0.328 1069 -
obs--95.41 %
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)
12.22430.1155-0.75485.09971.51375.5102-0.1275-0.04840.0328-0.02230.3561-0.2017-0.21590.1949-0.22860.18650.0640.01720.0795-0.02090.01659.96712.5277.036
24.52190.6782.0742.4166-0.34755.57460.3337-0.1448-0.25190.018-0.1675-0.01490.2079-0.315-0.16620.25530.0595-0.00220.05750.01880.02221.228-10.05423.583
33.2303-0.21780.22055.01751.4324.9216-0.1076-0.08140.0752-0.07860.22930.1547-0.3066-0.1856-0.12180.23290.09580.01960.11520.00720.01743.13915.5996.474
45.2071-0.16852.45242.7650.51714.94290.1467-0.19140.2207-0.078-0.15360.0035-0.1835-0.3940.00690.30610.09030.01390.0610.00650.022118.146-2.8824.066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 74
2X-RAY DIFFRACTION2B18 - 74
3X-RAY DIFFRACTION3C19 - 74
4X-RAY DIFFRACTION4D19 - 73

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