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3do7

X-ray structure of a NF-kB p52/RelB/DNA complex

Method: X-RAY DIFFRACTION Dmax: 110.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Avian reticuloendotheliosis viral (V-rel) oncogene related B

Mus musculus

UniProt Q8VE46

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 88–383 Fragment：RHR (UNP residues 88-383) 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3' × 2 Nuclear factor NF-kappa-B p100 subunit × 1 （Q00653） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q8VE46_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–296； UniProt 88–383

Nuclear factor NF-kappa-B p100 subunit

Homo sapiens

UniProt Q00653

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain B； UniProt 37–329 Fragment：RHR (UNP residues 37-329) 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3' × 2 Avian reticuloendotheliosis viral (V-rel) oncogene related B × 1 （Q8VE46） 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

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 3DO7 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 mutation/modification Different oligomeric state 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 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
4OT9 crystal structure of the C-terminal domain of p100/NF-kB2 Deposited 2014-02-13 Different construct 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 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 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 construct Different mutation/modification Different oligomeric state 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
7VUP Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment Deposited 2021-11-04 Different construct Different mutation/modification Different oligomeric state 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, 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
7VUQ Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment Deposited 2021-11-04 Different construct Different mutation/modification Different oligomeric state 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, 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 mutation/modification Different oligomeric state 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 3
Chains and sequence ranges Author chain B； PDBConstruct 1–293； UniProt 37–329

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3do7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3do7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3do7
Deposition date deposition_date2008-07-03
Structure title titleX-ray structure of a NF-kB p52/RelB/DNA complex
Keywords keywords;PROTEIN-DNA COMPLEX, Nucleus, Activator, Alternative splicing, ANK repeat, Chromosomal rearrangement, Cytoplasm, Disease mutation, DNA-binding, Phosphoprotein, Polymorphism, Proto-oncogene, Transcription, Transcription regulation, Ubl conjugation, TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.65 Å
Radius of gyration Rg (electron density) rg_electron32.02 Å
Forward intensity I(0) i0110124000.00
Molecular weight molecular_weight75147.0 kDa
Excluded volume excluded_volume90691 ų
Envelope volume envelope_volume129380 ų
Hydration-shell volume shell_volume35093 ų
Envelope diameter envelope_diameter118.2 Å
Shell Rg shell_rg36.94 Å
Envelope Rg envelope_rg32.96 Å
Shape Rg shape_rg32.06 Å
Total Rg total_rg32.32 Å
Total atoms total_atoms5239
Residues n_residues621
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.0 Å
Rg (real space) rg_real31.78 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real1.1010e+08
I(0) uncertainty (real space) i0_real_error1.5060e+06
Rg (reciprocal space) rg_reciprocal31.72 Å
I(0) (reciprocal space) i0_reciprocal110100000.0000
Solution quality estimate total_estimate0.8707
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.2 Å
Skewness Skewness skewness0.462
Kurtosis Kurtosis kurtosis-0.154
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15340000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3do7a1
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain
Domain ID domain_idd3do7a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd3do7b1
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.5 — p53-like transcription factors
Family Family familyb.2.5.3 — Rel/Dorsal transcription factors, DNA-binding domain
Domain ID domain_idd3do7b2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id3do7A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id3do7A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3do7B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily340 — Rel homology domain (RHD), DNA-binding domain
Domain ID domain_id3do7B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)