8pk5

INTS13-INTS14 complex with ZNF609

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD

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

Integrator complex subunit 13

Homo sapiens

UniProt Q9NVM9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–706 Not recorded Integrator complex subunit 14,Zinc finger protein 609 × 1 (Q96SY0,O15014) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003 Resolution 2.50 Å R-free 0.214

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.

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

View Construct and Data Evidence
UniProt name INT13_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 13–718; UniProt 1–706

Integrator complex subunit 14,Zinc finger protein 609

Homo sapiens

UniProt O15014

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 25–41 Not recorded Integrator complex subunit 13 × 1 (Q9NVM9) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003 Resolution 2.50 Å R-free 0.214

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 ZN609_HUMAN
Isoform O15014-1
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 522–538; UniProt 25–41

Integrator complex subunit 14,Zinc finger protein 609

Homo sapiens

UniProt Q96SY0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–518 Not recorded Integrator complex subunit 13 × 1 (Q9NVM9) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003 Resolution 2.50 Å R-free 0.214

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.

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

View Construct and Data Evidence
UniProt name INT14_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–518; UniProt 1–518

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 8pk5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8pk5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8pk5
Deposition date deposition_date2023-06-25
Structure title titleINTS13-INTS14 complex with ZNF609
Keywords keywordsProtein Complex, RNA BINDING, STRUCTURAL PROTEIN, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.79
Radius of gyration Rg (electron density) rg_electron36.08
Forward intensity I(0) i0199271000.00
Molecular weight molecular_weight113550.0 kDa
Excluded volume excluded_volume141970 ų
Envelope volume envelope_volume186520 ų
Hydration-shell volume shell_volume44703 ų
Envelope diameter envelope_diameter124.8
Shell Rg shell_rg40.94
Envelope Rg envelope_rg35.81
Shape Rg shape_rg36.04
Total Rg total_rg36.53
Total atoms total_atoms7968
Residues n_residues1029
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 dmax119.2
Rg (real space) rg_real36.76
Rg uncertainty (real space) rg_real_error0.74
I(0) (real space) i0_real1.9930e+08
I(0) uncertainty (real space) i0_real_error3.1000e+06
Rg (reciprocal space) rg_reciprocal36.78
I(0) (reciprocal space) i0_reciprocal199300000.0000
Solution quality estimate total_estimate0.8992
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4
Skewness Skewness skewness0.233
Kurtosis Kurtosis kurtosis-0.593
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30950000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.895

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)