SAXSdb — 9lc2

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear factor 1 A-type

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 13–175	Not recorded	;DNA (5'-D(APGPTPTPGPGPCPAPAPGPAPTPGPCPCPAPTPC)-3') ; × 1 ;DNA (5'-D(GPAPTPGPGPCPAPTPCPTPTPGPCPCPAPAPCPT)-3') ; × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris (pH 7.0), 20% (w/v) PEG 2000	Resolution 2.70 Å R-free 0.259
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 13–175	Not recorded	;DNA (5'-D(APGPTPTPGPGPCPAPAPGPAPTPGPCPCPAPTPC)-3') ; × 1 ;DNA (5'-D(GPAPTPGPGPCPAPTPCPTPTPGPCPCPAPAPCPT)-3') ; × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris (pH 7.0), 20% (w/v) PEG 2000	Resolution 2.70 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9LC2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9JH2 Crystal Structure of NFIA in Complex with DNA containing the TGGCA Motif Deposited 2024-09-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 13–175（163 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris Propane (pH 7.0), and 1.5 M Ammonium Sulfate	Resolution 2.30 Å R-free 0.283
9JH4 Crystal Structure of NFIA DNA-binding Domain Deposited 2024-09-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13–175（163 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES (pH 9.5), and 30% (w/v) PEG 3000	Resolution 3.20 Å R-free 0.297
9JH4 Crystal Structure of NFIA DNA-binding Domain Deposited 2024-09-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 13–175（163 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES (pH 9.5), and 30% (w/v) PEG 3000	Resolution 3.20 Å R-free 0.297
9JH4 Crystal Structure of NFIA DNA-binding Domain Deposited 2024-09-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 13–175（163 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES (pH 9.5), and 30% (w/v) PEG 3000	Resolution 3.20 Å R-free 0.297
9XVF Crystal structure of NFIA monomer bound to DNA Deposited 2025-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 10–174（165 aa） Chain B 10–174（165 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；5% (v/v) (+/-)-2-methyl-2,4-pentanediol, 0.1 M HEPES (pH 7.5), and 10% (w/v) PEG 10000	Resolution 2.60 Å R-free 0.248
9XVQ Crystal structure of the NFIA-N0 DNA complex Deposited 2025-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 10–238（229 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium phosphate dibasic dihydrate and 20% (w/v) PEG 3350	Resolution 1.76 Å R-free 0.222

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NFIA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–165； UniProt 13–175 Author chain B； PDBConstruct 3–165； UniProt 13–175

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9lc2
Deposition date deposition_date	2025-01-03
Structure title title	Crystal Structure of NFIA in Complex with DNA Containing the TGGCA(N3)TGCCA Motif
Keywords keywords	NFIA, Lipid metabolism, Transcription factor, DNA binding protein; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.30 Å
Radius of gyration Rg (electron density) rg_electron	35.44 Å
Forward intensity I(0) i0	86828100.00
Molecular weight molecular_weight	60720.0 kDa
Excluded volume excluded_volume	70200 Å³
Envelope volume envelope_volume	106880 Å³
Hydration-shell volume shell_volume	26895 Å³
Envelope diameter envelope_diameter	113.5 Å
Shell Rg shell_rg	39.30 Å
Envelope Rg envelope_rg	34.22 Å
Shape Rg shape_rg	35.43 Å
Total Rg total_rg	35.75 Å
Total atoms total_atoms	4201
Residues n_residues	400
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	113.9 Å
Rg (real space) rg_real	35.55 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	8.6830e+07
I(0) uncertainty (real space) i0_real_error	1.5860e+06
Rg (reciprocal space) rg_reciprocal	35.40 Å
I(0) (reciprocal space) i0_reciprocal	86820000.0000
Solution quality estimate total_estimate	0.8120
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.911
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4248000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.656; Smooth: 0.845

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Nuclear factor 1 A-type
Molecular weight formula_weight	19272.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4305

GSHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEYREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLDLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKEL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APGPTPTPGPGPCPAPAPGPAPTPGPCPCPAPTPC)-3') ;
Molecular weight formula_weight	5540.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E

AGTTGGCAAGATGCCATC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(GPAPTPGPGPCPAPTPCPTPTPGPCPCPAPAPCPT)-3') ;
Molecular weight formula_weight	5491.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

GATGGCATCTTGCCAACT

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

▶

8. Citations (1)

▶

Unit-cell length a length_a	49.075 Å
Unit-cell length b length_b	78.141 Å
Unit-cell length c length_c	88.123 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	39.070 Å
R factor r_factor	0.2078
R_work r_work	0.2047
R_free r_free	0.2594

fit	/app/data/saxs_computation/lc/9lc2/9lc2.fit
pddf	/app/data/pr_computation/lc/9lc2/9lc2.pr.out
profile	/app/data/saxs_computation/lc/9lc2/9lc2.dat

Crystal Structure of NFIA in Complex with DNA Containing the TGGCA(N3)TGCCA Motif

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear factor 1 A-type

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)