5xoc

Crystal structure of human Smad3-FoxH1 complex

Method: X-RAY DIFFRACTION Dmax: 78.2 Å Quality: GOOD

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

Mothers against decapentaplegic homolog 3

Homo sapiens

UniProt P84022

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 220–416 Fragment:UNP residues 220-416 Thioredoxin 1,Forkhead box protein H1 × 3 (P0AA25,O75593) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.4;293 K;0.1 M citrate pH 5.4, 0.8% ethylene imine polymer and 0.5 M NaCl Resolution 2.40 Å R-free 0.235

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.

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMAD3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–199; UniProt 220–416

Thioredoxin 1,Forkhead box protein H1

Homo sapiens

UniProt O75593

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 322–345 Fragment:UNP residues 2-109,UNP residues 322-345 Mothers against decapentaplegic homolog 3 × 3 (P84022) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.4;293 K;0.1 M citrate pH 5.4, 0.8% ethylene imine polymer and 0.5 M NaCl Resolution 2.40 Å R-free 0.235

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FOXH1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 118–141; UniProt 322–345

Thioredoxin 1,Forkhead box protein H1

Homo sapiens

UniProt P0AA25

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–109 Fragment:UNP residues 2-109,UNP residues 322-345 Mothers against decapentaplegic homolog 3 × 3 (P84022) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.4;293 K;0.1 M citrate pH 5.4, 0.8% ethylene imine polymer and 0.5 M NaCl Resolution 2.40 Å R-free 0.235

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.

52 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 8–115; UniProt 2–109

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 5xoc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xoc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xoc
Deposition date deposition_date2017-05-27
Structure title titleCrystal structure of human Smad3-FoxH1 complex
Keywords keywordstranscription factor, complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.11
Radius of gyration Rg (electron density) rg_electron23.36
Forward intensity I(0) i022404900.00
Molecular weight molecular_weight36385.0 kDa
Excluded volume excluded_volume45659 ų
Envelope volume envelope_volume55197 ų
Hydration-shell volume shell_volume20921 ų
Envelope diameter envelope_diameter79.7
Shell Rg shell_rg28.84
Envelope Rg envelope_rg23.27
Shape Rg shape_rg23.35
Total Rg total_rg24.09
Total atoms total_atoms2560
Residues n_residues327
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 dmax78.2
Rg (real space) rg_real24.21
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real2.2400e+07
I(0) uncertainty (real space) i0_real_error3.1130e+05
Rg (reciprocal space) rg_reciprocal24.19
I(0) (reciprocal space) i0_reciprocal22400000.0000
Solution quality estimate total_estimate0.8887
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.2
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5200000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5xoca_
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

CATH v4.4 (2 domains)

Domain ID domain_id5xocA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily10
Domain ID domain_id5xocB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin

8. Citations (1)

9. Files and Curves (10)