PDB-9g19: Structure of the Nothoceros aenigmaticus LFY DNA-binding domain b...

ID or keywords:

Entry

Database: PDB / ID: 9g19

Title

Structure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA

Components

(DNA (25-MER)) x 2
Floricaula/leafy-like transcription factor

Keywords

GENE REGULATION / transcription factor / DNA-binding / protein-DNA complex

Function / homology

Function and homology information

regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function

Biological species

Nothoceros aenigmaticus (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.092 Å

Authors

Zubieta, C. / Verhage, L. / Nanao, M.H. / Parcy, F.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Structure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA
Authors: Zubieta, C. / Verhage, L. / Nanao, M.H. / Parcy, F.

History

Deposition	Jul 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9g19.cif.gz	247.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9g19.ent.gz	153.3 KB	Display	PDB format
PDBx/mmJSON format	9g19.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9g19_validation.pdf.gz	452.6 KB	Display	wwPDB validaton report
Full document	9g19_full_validation.pdf.gz	462.5 KB	Display
Data in XML	9g19_validation.xml.gz	17.2 KB	Display
Data in CIF	9g19_validation.cif.gz	22.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g1/9g19 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/9g19	HTTPS FTP

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Related structure data

Related structure data	9fwyC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
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#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
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#253 - Jan 2021
Expressome
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#112 - Apr 2009
Oct and Sox Transcription Factors
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#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
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#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
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#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
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similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Floricaula/leafy-like transcription factor

B: Floricaula/leafy-like transcription factor

C: DNA (25-MER)

D: DNA (25-MER)

54.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis, EMSA with DNA

Unit cell

Length a, b, c (Å)	71.708, 154.104, 53.062
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Floricaula/leafy-like transcription factor Mass: 19446.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nothoceros aenigmaticus (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: W8EDT4
#2: DNA chain	DNA (25-MER) Mass: 7632.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nothoceros aenigmaticus (plant)
#3: DNA chain	DNA (25-MER) Mass: 7727.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nothoceros aenigmaticus (plant)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.48 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M lithium chloride, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 3.09→43.7 Å / Num. obs: 11139 / % possible obs: 98 % / Redundancy: 5.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.106 / R_pim(I) all: 0.051 / R_rim(I) all: 0.118 / Net I/σ(I): 7.4 / Num. measured all: 59477
Reflection shell	Resolution: 3.09→3.2 Å / % possible obs: 87.6 % / Redundancy: 5.3 % / R_merge(I) obs: 1.438 / Num. measured all: 5087 / Num. unique obs: 952 / CC_1/2: 0.809 / R_pim(I) all: 0.67 / R_rim(I) all: 1.591 / Net I/σ(I) obs: 0.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
SCALA		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.092→30.002 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.902 / SU B: 102.648 / SU ML: 0.741 / Cross valid method: THROUGHOUT / ESU R Free: 0.552
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3031	556	5.037 %	RANDOM
R_work	0.2429	10482	-	-
all	0.246	-	-	-
obs	-	11038	97.492 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 155.204 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.341 Å²	-0 Å²	0 Å²
2-	-	7.868 Å²	-0 Å²
3-	-	-	-2.527 Å²

Refinement step

Cycle: LAST / Resolution: 3.092→30.002 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2438	1017	0	1	3456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.011	3637
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2893
X-RAY DIFFRACTION	r_angle_refined_deg	1.038	1.839	5124
X-RAY DIFFRACTION	r_angle_other_deg	0.328	1.743	6697
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.586	5	308
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.306	5	14
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.209	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.644	10	435
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	10.625	10	114
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	550
X-RAY DIFFRACTION	r_chiral_restr_other	0.012	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3553
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	758
X-RAY DIFFRACTION	r_nbd_refined	0.263	0.2	979
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.243	0.2	2976
X-RAY DIFFRACTION	r_nbtor_refined	0.215	0.2	1676
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1563
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	132
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.101	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.257	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.447	0.2	29
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	12.665	7.182	1238
X-RAY DIFFRACTION	r_mcbond_other	12.663	7.183	1238
X-RAY DIFFRACTION	r_mcangle_it	18.576	12.827	1544
X-RAY DIFFRACTION	r_mcangle_other	18.571	12.834	1545
X-RAY DIFFRACTION	r_scbond_it	12.329	6.916	2399
X-RAY DIFFRACTION	r_scbond_other	12.329	6.916	2399
X-RAY DIFFRACTION	r_scangle_it	18.559	12.305	3580
X-RAY DIFFRACTION	r_scangle_other	18.557	12.305	3581
X-RAY DIFFRACTION	r_lrange_it	26.576	79.792	14941
X-RAY DIFFRACTION	r_lrange_other	26.575	79.801	14942

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.092-3.172	0.345	35	0.43	607	0.426	810	0.942	0.902	79.2593	0.418
3.172-3.258	0.476	44	0.346	727	0.353	790	0.888	0.952	97.5949	0.362
3.258-3.351	0.311	29	0.28	729	0.281	777	0.959	0.973	97.5547	0.307
3.351-3.453	0.337	38	0.277	688	0.28	738	0.948	0.961	98.374	0.298
3.453-3.564	0.48	37	0.313	700	0.321	745	0.796	0.95	98.9262	0.329
3.564-3.688	0.424	28	0.314	656	0.318	689	0.939	0.942	99.2743	0.326
3.688-3.825	0.36	29	0.295	644	0.298	681	0.946	0.952	98.8253	0.312
3.825-3.978	0.284	26	0.264	622	0.265	654	0.939	0.968	99.0826	0.285
3.978-4.152	0.447	28	0.253	607	0.261	637	0.863	0.964	99.686	0.276
4.152-4.35	0.328	35	0.254	566	0.259	604	0.954	0.955	99.5033	0.28
4.35-4.58	0.242	37	0.241	537	0.241	578	0.969	0.967	99.308	0.268
4.58-4.851	0.233	18	0.249	536	0.249	557	0.973	0.963	99.4614	0.306
4.851-5.176	0.25	39	0.221	477	0.223	518	0.946	0.971	99.6139	0.27
5.176-5.577	0.258	30	0.231	464	0.233	494	0.968	0.967	100	0.298
5.577-6.089	0.328	18	0.226	433	0.23	451	0.945	0.968	100	0.29
6.089-6.772	0.246	20	0.22	403	0.222	423	0.969	0.971	100	0.304
6.772-7.755	0.218	22	0.199	354	0.2	377	0.966	0.972	99.7347	0.287
7.755-9.343	0.239	13	0.182	305	0.184	322	0.97	0.979	98.7578	0.291
9.343-12.615	0.25	22	0.177	251	0.182	273	0.957	0.979	100	0.306
12.615-30.002	0.449	8	0.265	176	0.274	186	0.909	0.945	98.9247	0.546

Refinement TLS params.

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

ID	L11 (°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)
1	1.0874	-0.9982	-0.9245	1.4749	0.0325	2.2486	-0.0206	0.0184	-0.1395	0.1807	-0.0258	-0.0036	0.0865	-0.227	0.0464	1.3845	-0.0169	-0.0434	0.4123	-0.0742	1.097	-13.787	8.236	-7.182
2	3.0654	-0.0554	0.3425	1.5447	0.4023	0.1817	0.082	-0.7607	-0.2175	0.0643	-0.0823	0.3203	-0.1912	-0.1279	0.0003	1.4318	0.0667	0.067	0.4876	0.1165	1.3066	-42.328	33.837	-14.7
3	0.8106	-0.4454	-0.5084	2.5549	-0.0577	0.936	-0.1515	0.1866	-0.0102	0.1746	0.3148	0.5492	0.0468	0.1037	-0.1633	1.5155	0.1348	-0.0486	0.3136	-0.1877	1.5281	-22.931	21.951	-21.523
4	1.327	0.0946	-0.9526	0.3421	0.066	1.0976	-0.1765	0.1317	0.0338	0.3691	0.1736	0.4852	0.0673	0.2636	0.0029	1.5251	0.1723	-0.1462	0.3693	-0.0887	1.4693	-22.161	26.208	-19.418

Refinement TLS group

Selection: ALL

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