2o93

Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element

Method: X-RAY DIFFRACTION Dmax: 127.5 Å Quality: GOOD

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

actor of activated T-cells, cytoplasmic 2

Homo sapiens

UniProt Q13469

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 × 3 DNA 2 PDB declaration: pentameric(5) Consistent with all polymer counts Chain L; UniProt 392–678 Chain M; UniProt 392–678 Chain O; UniProt 392–678 Fragment:RHR domain kappaB enhancer element, DNA 25-mer × 1 kappaB enhancer element, DNA 25-mer × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;291 K;50mM Hepes pH 7.0, 15mM Magnesium Acetate, 250mM Ammonium Acetate, 7.5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.05 Å R-free 0.283

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.

11 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NFAC2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain L; PDBConstruct 15–301; UniProt 392–678 Author chain M; PDBConstruct 15–301; UniProt 392–678 Author chain O; PDBConstruct 15–301; UniProt 392–678

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 2o93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2o93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2o93
Deposition date deposition_date2006-12-13
Structure title titleCrystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element
Keywords keywordsIG domain; Protein-DNA complex; double helix, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.94
Radius of gyration Rg (electron density) rg_electron38.66
Forward intensity I(0) i0236737000.00
Molecular weight molecular_weight112670.0 kDa
Excluded volume excluded_volume136170 ų
Envelope volume envelope_volume196920 ų
Hydration-shell volume shell_volume44087 ų
Envelope diameter envelope_diameter135.4
Shell Rg shell_rg42.76
Envelope Rg envelope_rg37.71
Shape Rg shape_rg38.69
Total Rg total_rg38.83
Total atoms total_atoms7866
Residues n_residues908
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax127.5
Rg (real space) rg_real37.91
Rg uncertainty (real space) rg_real_error1.49
I(0) (real space) i0_real2.3670e+08
I(0) uncertainty (real space) i0_real_error4.1250e+06
Rg (reciprocal space) rg_reciprocal37.93
I(0) (reciprocal space) i0_reciprocal236700000.0000
Solution quality estimate total_estimate0.8976
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12040000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.941

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd2o93l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd2o93l2
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_idd2o93m1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd2o93m2
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_idd2o93m3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2o93o1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
Domain ID domain_idd2o93o2
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

CATH v4.4 (6 domains)

Domain ID domain_id2o93L01
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_id2o93L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2o93M01
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_id2o93M02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2o93O01
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_id2o93O02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)