SAXSdb — 7vup

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

Nuclear factor NF-kappa-B p52 subunit

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–398 Chain B； UniProt 1–398	Not recorded	;DNA (5'-D(CPAPAPGPGPGPGPAPCPTPCPCPCPCPCPTPT)-3') ; × 1 ;DNA (5'-D(APAPGPGPGPGPGPAPGPTPCPCPCPCPTPTPG)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350	Resolution 3.40 Å R-free 0.286

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 7VUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3Q HUMAN NF-KAPPA-B P52 BOUND TO DNA Deposited 1998-01-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 37–327（291 aa） Chain B 37–327（291 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；THE PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE RESERVOIR SOLUTION CONTAINED 5% PEG 4000, 5 MM MGSO4, 50 MM MES PH 6.0 AND 3 MM DTT. DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR SOLUTION., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.320
2D96 Solution structure of the Death domain of Nuclear factor NF-kappa-B p100 Deposited 2005-12-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 766–861（96 aa） Fragment：death domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.15mM death domain U-15N, 13C, 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
3DO7 X-ray structure of a NF-kB p52/RelB/DNA complex Deposited 2008-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 37–329（293 aa） Fragment：RHR (UNP residues 37-329)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；6% PEG 4000, 50 mM NaCl, 0.1% BOG, 10 mM DTT, 10 mM NaCitrate and 2 mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.273
4OT9 crystal structure of the C-terminal domain of p100/NF-kB2 Deposited 2014-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–765（359 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10% PEG 4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.272
4OT9 crystal structure of the C-terminal domain of p100/NF-kB2 Deposited 2014-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 407–765（359 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；10% PEG 4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.35 Å R-free 0.272
5ZMC Structural Basis for Reactivation of -146C>T Mutant TERT Promoter by cooperative binding of p52 and ETS1/2 Deposited 2018-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 35–329（295 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M HEPES pH 7.0 and 2.0 M Ammonium sulphate	Resolution 2.99 Å R-free 0.288
7CLI Structure of NF-kB p52 homodimer bound to P-Selectin kB DNA fragment Deposited 2020-07-21	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–398（398 aa） Chain B 1–398（398 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Sodium malonate, pH 4.0, 0.2M CsCl, 5% PEG 3350	Resolution 3.00 Å R-free 0.275
7VUQ Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment Deposited 2021-11-04	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–398（398 aa） Chain B 1–398（398 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium malonate, pH 4.0, 50mM CsCl, 2.5% PEG 3350	Resolution 3.10 Å R-free 0.249
7W7L Structure of NF-kB p52 homodimer bound to 13-mer A/T-centric P-Selectin kB DNA fragment Deposited 2021-12-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50mM MES, pH 6.0, 10mM MgCl2, 10% PEG 3350	Resolution 3.00 Å R-free 0.258

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NFKB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–398； UniProt 1–398 Author chain B； PDBConstruct 1–398； UniProt 1–398

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7vup
Deposition date deposition_date	2021-11-04
Structure title title	Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment
Keywords keywords	DNA-protein complex, transcription factor, TRANSCRIPTION, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	31.16 Å
Radius of gyration Rg (electron density) rg_electron	31.80 Å
Forward intensity I(0) i0	113127000.00
Molecular weight molecular_weight	76827.0 kDa
Excluded volume excluded_volume	93038 Å³
Envelope volume envelope_volume	127960 Å³
Hydration-shell volume shell_volume	35078 Å³
Envelope diameter envelope_diameter	112.6 Å
Shell Rg shell_rg	36.81 Å
Envelope Rg envelope_rg	32.08 Å
Shape Rg shape_rg	31.84 Å
Total Rg total_rg	32.10 Å
Total atoms total_atoms	5359
Residues n_residues	626
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

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

Maximum dimension Dmax dmax	110.0 Å
Rg (real space) rg_real	31.22 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.1310e+08
I(0) uncertainty (real space) i0_real_error	1.8100e+06
Rg (reciprocal space) rg_reciprocal	31.20 Å
I(0) (reciprocal space) i0_reciprocal	113100000.0000
Solution quality estimate total_estimate	0.8631
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.7 Å
Skewness Skewness skewness	0.402
Kurtosis Kurtosis kurtosis	-0.207
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12030000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.946

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nuclear factor NF-kappa-B p52 subunit
Molecular weight formula_weight	43732.5 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	5359

MESCYNPGLDGIIEYDDFKLNSSIVEPKEPAPETADGPYLVIVEQPKQRGFRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSDPPRAHAHSLVGKQCSELGICAVSVGPKDMTAQFNNLGVLHVTKKNMMGTMIQKLQRQRLRSRPQGLTEAEQRELEQEAKELKKVMDLSIVRLRFSAFLRASDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSVRGGDEVYLLCDKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIERPVTVFLQLKRKRGGDVSDSKQFTYYPLVEDKEEVQRKRRKALPTFSQPFGGGSHMGGGSGGAAGGYGGAGGGGSLGFFPSSLAYSPYQSGAGPMGCY

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPAPAPGPGPGPGPAPCPTPCPCPCPCPCPTP*T)-3') ;
Molecular weight formula_weight	5437.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CAAGGGGACTCCCCCTTC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APAPGPGPGPGPGPAPGPTPCPCPCPCPTPTP*G)-3') ;
Molecular weight formula_weight	5597.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GAAGGGGGAGTCCCCTTG

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8. Citations (1)

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Unit-cell length a length_a	83.987 Å
Unit-cell length b length_b	84.289 Å
Unit-cell length c length_c	140.565 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	45.451 Å
R factor r_factor	—
R_work r_work	0.2712
R_free r_free	0.2858

fit	/app/data/saxs_computation/vu/7vup/7vup.fit
pddf	/app/data/pr_computation/vu/7vup/7vup.pr.out
profile	/app/data/saxs_computation/vu/7vup/7vup.dat

Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment

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

Nuclear factor NF-kappa-B p52 subunit

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)