3cbp

Set7/9-ER-Sinefungin complex

Method: X-RAY DIFFRACTION Dmax: 67.6 Å Quality: GOOD

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

Histone-lysine N-methyltransferase SETD7

Homo sapiens

UniProt Q8WTS6

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 111–366 Fragment:UNP residues 111-366 Estrogen receptor × 1 (P03372) SFG SINEFUNGIN × 1 BME BETA-MERCAPTOETHANOL × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, pH 8.00 Resolution 1.42 Å R-free 0.243

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.

31 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SETD7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–256; UniProt 111–366

Estrogen receptor

OrganismNot specified

UniProt P03372

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 298–307 Fragment:UNP residues 298-307 Histone-lysine N-methyltransferase SETD7 × 1 (Q8WTS6) SFG SINEFUNGIN × 1 BME BETA-MERCAPTOETHANOL × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, pH 8.00 Resolution 1.42 Å R-free 0.243

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.

434 other PDB entries and 522 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ESR1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–10; UniProt 298–307

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 3cbp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3cbp
Deposition date deposition_date2008-02-22
Structure title titleSet7/9-ER-Sinefungin complex
Keywords keywords;Estrogen Receptor, protein lysine methylation, Activator, Chromatin regulator, Chromosomal protein, Methyltransferase, Nucleus, S-adenosyl-L-methionine, Transcription, Transcription regulation, Transferase, DNA-binding, Lipid-binding, Metal-binding, Phosphoprotein, Steroid-binding, Zinc-finger, TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX ;; TRANSFERASE/TRANSFERASE RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.92
Radius of gyration Rg (electron density) rg_electron18.90
Forward intensity I(0) i014189000.00
Molecular weight molecular_weight27646.0 kDa
Excluded volume excluded_volume34254 ų
Envelope volume envelope_volume39580 ų
Hydration-shell volume shell_volume17947 ų
Envelope diameter envelope_diameter71.8
Shell Rg shell_rg24.89
Envelope Rg envelope_rg19.44
Shape Rg shape_rg18.90
Total Rg total_rg19.80
Total atoms total_atoms1943
Residues n_residues243
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 dmax67.6
Rg (real space) rg_real19.96
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real1.4190e+07
I(0) uncertainty (real space) i0_real_error1.9650e+05
Rg (reciprocal space) rg_reciprocal19.95
I(0) (reciprocal space) i0_reciprocal14190000.0000
Solution quality estimate total_estimate0.7878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.8
Skewness Skewness skewness0.450
Kurtosis Kurtosis kurtosis-0.105
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3320000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cbpa1
Class classb — All beta proteins
Fold Fold foldb.76 — open-sided beta-meander
Superfamily Superfamily superfamilyb.76.2 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Family Family familyb.76.2.1 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Domain ID domain_idd3cbpa2
Class classb — All beta proteins
Fold Fold foldb.85 — beta-clip
Superfamily Superfamily superfamilyb.85.7 — SET domain
Family Family familyb.85.7.1 — Histone lysine methyltransferases

CATH v4.4 (2 domains)

Domain ID domain_id3cbpA01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Domain ID domain_id3cbpA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology270 — Beta-clip-like
Homologous superfamily homologous superfamily10 — SET domain

8. Citations (1)

9. Files and Curves (10)