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2edb

Solution structure of the fourth fibronectin type III domain of human Netrin receptor DCC

Method: SOLUTION NMR Dmax: 44.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Netrin receptor DCC

Homo sapiens

UniProt P43146

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 716–818 Fragment：fourth fn3 domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O' | 90% H2O/10% 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.

Other PDB Difference from Current Entry 2EDB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2ED7 Solution structure of the first fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 419–524（106 aa） Fragment：first fn3 domain, Fibronectin type-III 1
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2ED8 Solution structure of the second fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 528–620（93 aa） Fragment：second fn3 domain, Fibronectin type-III 2
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2ED9 Solution structure of the third fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 602–718（117 aa） Fragment：third fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.5mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O' | 90% H2O/10% D2O
Resolution not provided
2EDD Solution structure of the fifth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 833–942（110 aa） Fragment：fifth fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.2mM sample U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2EDE Solution structure of the sixth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 944–1044（101 aa） Fragment：sixth fn3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.3mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3AU4 Structure of the human myosin-X MyTH4-FERM cassette bound to its specific cargo, DCC Deposited 2011-01-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1390–1447（58 aa） Fragment：P3 domain, UNP residues 1390-1447
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM maric acid-MES-Tris (MMT) buffer, 2% PEG 1500, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.233
4URT The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC Deposited 2014-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 844–1043（200 aa） Fragment：FN5-FN6, RESIDUES 844-1043
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 18 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M MES PH 6.0, 0.15M AMMONIUM SULFATE AND 15% (W/V) PEG 4000
Resolution 3.10 Å R-free 0.265
5X83 Structure of DCC FN456 domains Deposited 2017-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 721–815（95 aa） Fragment：UNP residues 721-815
Chain B 844–1043（200 aa） Fragment：UNP residues 844-1043
Chain C 721–815（95 aa） Fragment：UNP residues 721-815
Chain D 844–1043（200 aa） Fragment：UNP residues 844-1043
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.1M Sodium Phosphate Monobasic Monohydrate, 0.1M Potassium Phosphate Monobasic, 0.1M MES Monohydrate pH 6.5, 2.0M Sodium Chloride
Resolution 3.00 Å R-free 0.278

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

View Construct and Data Evidence
UniProt name DCC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–110； UniProt 716–818

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 2edb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2edb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2edb
Deposition date deposition_date2007-02-14
Structure title titleSolution structure of the fourth fibronectin type III domain of human Netrin receptor DCC
Keywords keywords;Tumor suppressor protein DCC, Colorectal cancer suppressor, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, APOPTOSIS ;; APOPTOSIS
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.81 Å
Radius of gyration Rg (electron density) rg_electron16.15 Å
Forward intensity I(0) i0942983000.00
Molecular weight molecular_weight248890.0 kDa
Excluded volume excluded_volume306680 ų
Envelope volume envelope_volume39082 ų
Hydration-shell volume shell_volume16230 ų
Envelope diameter envelope_diameter87.3 Å
Shell Rg shell_rg27.30 Å
Envelope Rg envelope_rg23.32 Å
Shape Rg shape_rg16.12 Å
Total Rg total_rg16.47 Å
Total atoms total_atoms34380
Residues n_residues2320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax44.5 Å
Rg (real space) rg_real15.54 Å
Rg uncertainty (real space) rg_real_error0.07 Å
I(0) (real space) i0_real8.9560e+08
I(0) uncertainty (real space) i0_real_error8.8740e+06
Rg (reciprocal space) rg_reciprocal17.06 Å
I(0) (reciprocal space) i0_reciprocal943000000.0000
Solution quality estimate total_estimate0.6792
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.2 Å
Skewness Skewness skewness0.395
Kurtosis Kurtosis kurtosis-0.488
Angular range angular_range— – 0.4750 Å−1
Current regularization parameter α current_alpha2.9190
Highest regularization parameter α highest_alpha422800.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.962; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2edbA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)