SAXSdb — 5x83

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

Netrin receptor DCC

Homo sapiens

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 721–815 Chain B； UniProt 844–1043 Chain C； UniProt 721–815 Chain D； UniProt 844–1043	Fragment：UNP residues 721-815 Fragment：UNP residues 844-1043	No other associated polymer	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

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 5X83	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
2EDB Solution structure of the fourth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 716–818（103 aa） Fragment：fourth 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
2EDD Solution structure of the fifth fibronectin type III domain of human Netrin receptor DCC Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion 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

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, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 721–815 Author chain C； PDBConstruct 1–95； UniProt 721–815 Author chain B； PDBConstruct 2–201； UniProt 844–1043 Author chain D； PDBConstruct 2–201； UniProt 844–1043

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5x83
Deposition date deposition_date	2017-02-28
Structure title title	Structure of DCC FN456 domains
Keywords keywords	DCC, Netrin-1, axon guidance, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	41.49 Å
Radius of gyration Rg (electron density) rg_electron	42.52 Å
Forward intensity I(0) i0	65396700.00
Molecular weight molecular_weight	65652.0 kDa
Excluded volume excluded_volume	82566 Å³
Envelope volume envelope_volume	118650 Å³
Hydration-shell volume shell_volume	27368 Å³
Envelope diameter envelope_diameter	159.8 Å
Shell Rg shell_rg	38.43 Å
Envelope Rg envelope_rg	43.15 Å
Shape Rg shape_rg	42.51 Å
Total Rg total_rg	42.27 Å
Total atoms total_atoms	4627
Residues n_residues	586
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.9 Å
Rg (real space) rg_real	37.72 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	6.2100e+07
I(0) uncertainty (real space) i0_real_error	8.7830e+05
Rg (reciprocal space) rg_reciprocal	41.50 Å
I(0) (reciprocal space) i0_reciprocal	65340000.0000
Solution quality estimate total_estimate	0.6596
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.715
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.8352
Highest regularization parameter α highest_alpha	2800000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.958; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.764; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Netrin receptor DCC
Molecular weight formula_weight	12021.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4627

DESQVPDQPSSLHVRPQTNCIIMSWTPPLNPNIVVRGYIIGYGVGSPYAETVRVDSKQRYYSIERLESSSHYVISLKAFNNAGEGVPLYESATTRGSGGSGGSGGSGGSGGSGGSG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Netrin receptor DCC
Molecular weight formula_weight	23357.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GMLPPVGVQAVALTHDAVRVSWADNSVPKNQKTSEVRLYTVRWRTSFSASAKYKSEDTTSLSYTATGLKPNTMYEFSVMVTKNRRSSTWSMTAHATTYEAAPTSAPKDLTVITREGKPRAVIVSWQPPLEANGKITAYILFYTLDKNIPIDDWIMETISGDRLTHQIMDLNLDTMYYFRIQARNSKGVGPLSDPILFRTLKLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5x83A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5x83B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5x83B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5x83C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5x83D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5x83D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	53.459 Å
Unit-cell length b length_b	126.971 Å
Unit-cell length c length_c	57.162 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.997 Å
Low-resolution limit resolution_low	42.142 Å
R factor r_factor	0.2237
R_work r_work	0.2208
R_free r_free	0.2778

fit	/app/data/saxs_computation/x8/5x83/5x83.fit
pddf	/app/data/pr_computation/x8/5x83/5x83.pr.out
profile	/app/data/saxs_computation/x8/5x83/5x83.dat

Structure of DCC FN456 domains

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

Netrin receptor DCC

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)