1mr1

Crystal Structure of a Smad4-Ski Complex

Method: X-RAY DIFFRACTION Dmax: 106.3 Å Quality: GOOD

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

Mothers against decapentaplegic homolog 4

Homo sapiens

UniProt Q13485

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 319–552 Fragment:MH2 domain Ski oncogene × 1 (P12755) ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.85 Å R-free 0.280
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 319–552 Fragment:MH2 domain Ski oncogene × 1 (P12755) ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.85 Å R-free 0.280

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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMAD4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–235; UniProt 319–552 Author chain B; PDBConstruct 2–235; UniProt 319–552

Ski oncogene

Homo sapiens

UniProt P12755

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 D; UniProt 219–313 Fragment:Smad4-binding domain Mothers against decapentaplegic homolog 4 × 1 (Q13485) ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.85 Å R-free 0.280
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 219–313 Fragment:Smad4-binding domain Mothers against decapentaplegic homolog 4 × 1 (Q13485) ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.85 Å R-free 0.280

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SKI_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 5–99; UniProt 219–313 Author chain D; PDBConstruct 5–99; UniProt 219–313

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 1mr1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1mr1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1mr1
Deposition date deposition_date2002-09-17
Structure title titleCrystal Structure of a Smad4-Ski Complex
Keywords keywordsSmad, Ski, cancer, TGF-b signaling, protein interaction, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.41
Radius of gyration Rg (electron density) rg_electron27.54
Forward intensity I(0) i076241500.00
Molecular weight molecular_weight66596.0 kDa
Excluded volume excluded_volume82579 ų
Envelope volume envelope_volume105740 ų
Hydration-shell volume shell_volume32276 ų
Envelope diameter envelope_diameter113.4
Shell Rg shell_rg34.28
Envelope Rg envelope_rg28.00
Shape Rg shape_rg27.51
Total Rg total_rg28.31
Total atoms total_atoms4668
Residues n_residues581
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 dmax106.3
Rg (real space) rg_real28.40
Rg uncertainty (real space) rg_real_error1.00
I(0) (real space) i0_real7.6240e+07
I(0) uncertainty (real space) i0_real_error1.1610e+06
Rg (reciprocal space) rg_reciprocal28.41
I(0) (reciprocal space) i0_reciprocal76240000.0000
Solution quality estimate total_estimate0.8344
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.2
Skewness Skewness skewness0.359
Kurtosis Kurtosis kurtosis-0.154
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12750000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.662; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1mr1a_
Class classb — All beta proteins
Fold Fold foldb.26 — SMAD/FHA domain
Superfamily Superfamily superfamilyb.26.1 — SMAD/FHA domain
Family Family familyb.26.1.1 — SMAD domain
Domain ID domain_idd1mr1b_
Class classb — All beta proteins
Fold Fold foldb.26 — SMAD/FHA domain
Superfamily Superfamily superfamilyb.26.1 — SMAD/FHA domain
Family Family familyb.26.1.1 — SMAD domain
Domain ID domain_idd1mr1c1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.217 — SAND domain-like
Superfamily Superfamily superfamilyd.217.1 — SAND domain-like
Family Family familyd.217.1.2 — SMAD4-binding domain of oncoprotein Ski
Domain ID domain_idd1mr1c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1mr1d1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.217 — SAND domain-like
Superfamily Superfamily superfamilyd.217.1 — SAND domain-like
Family Family familyd.217.1.2 — SMAD4-binding domain of oncoprotein Ski
Domain ID domain_idd1mr1d2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id1mr1A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily10
Domain ID domain_id1mr1B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily10
Domain ID domain_id1mr1C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology390 — SAND domain
Homologous superfamily homologous superfamily10 — SAND domain-like
Domain ID domain_id1mr1D00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology390 — SAND domain
Homologous superfamily homologous superfamily10 — SAND domain-like

8. Citations (1)

9. Files and Curves (10)