1j5n

Solution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA

Method: SOLUTION NMR Dmax: 57.7 Å Quality: GOOD

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

Nonhistone chromosomal protein 6A

Saccharomyces cerevisiae

UniProt P11632

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 1–93 Not recorded 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3' × 1 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3' × 1 SOLUTION NMR NMR measurement conditions:pH 5.8;310 K;Ionic strength (raw mmCIF value) 2 mM NaPO4, 10 mM NaCl;Pressure ambient NMR measurement conditions:pH 5.8;283 K;Ionic strength (raw mmCIF value) 2 mM NaPO4, 10 mM NaCl;Pressure ambient NMR sample composition:protein and DNA unlabeled, 2mM sample 90% H2O, 10% D2O or 100% D2O NMR sample composition:Uniform labeling with 15N of protein, DNA unlabeled, 2mM 90% H2O, 10% D2O NMR sample composition:Uniform labeling with 15N,13C of protein, DNA unlabeled, 2mM 100% D2O NMR sample composition:Uniform labeling with 15N,13C of DNA (both strands), protein unlabeled, 2mM 100% D2O NMR sample composition:Uniform labeling with 15N,13C of G-rich DNA strand and protein, C-rich DNA strand unlabeled, 2mM 100% D2O NMR sample composition:Uniform labeling with 15N,13C of C-rich DNA strand and protein, G-rich DNA strand unlabeled, 2mM 100% D2O Resolution not provided

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NHP6A_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–93; UniProt 1–93

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 1j5n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1j5n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1j5n
Deposition date deposition_date2002-05-15
Structure title titleSolution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA
Keywords keywordsHMG-BOX, HMGB, PROTEIN-DNA COMPLEX, ALPHA HELIX, DOUBLE HELIX, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier17.02
Radius of gyration Rg (electron density) rg_electron16.99
Forward intensity I(0) i03795370000.00
Molecular weight molecular_weight399630.0 kDa
Excluded volume excluded_volume448830 ų
Envelope volume envelope_volume42035 ų
Hydration-shell volume shell_volume19105 ų
Envelope diameter envelope_diameter64.5
Shell Rg shell_rg24.85
Envelope Rg envelope_rg18.75
Shape Rg shape_rg16.94
Total Rg total_rg17.18
Total atoms total_atoms49780
Residues n_residues2460
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 dmax57.7
Rg (real space) rg_real17.04
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real3.7950e+09
I(0) uncertainty (real space) i0_real_error4.6280e+07
Rg (reciprocal space) rg_reciprocal17.04
I(0) (reciprocal space) i0_reciprocal3795000000.0000
Solution quality estimate total_estimate0.8726
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.2
Skewness Skewness skewness0.412
Kurtosis Kurtosis kurtosis-0.163
Angular range angular_range— – 0.4700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1424000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.974

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1j5na_
Class classa — All alpha proteins
Fold Fold folda.21 — HMG-box
Superfamily Superfamily superfamilya.21.1 — HMG-box
Family Family familya.21.1.1 — HMG-box

CATH v4.4 (1 domains)

Domain ID domain_id1j5nA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily10 — High mobility group box domain

8. Citations (1)

9. Files and Curves (10)