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3afc

Mouse Semaphorin 6A extracellular domain

Method: X-RAY DIFFRACTION Dmax: 111.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Semaphorin-6A

Mus musculus

UniProt O35464

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 19–570 Chain B； UniProt 19–570 Fragment：sema and PSI domain (UNP residues 19-570) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22-24% (wt/vol) PEG 1500, 0.1M Tris-Cl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.50 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 3AFC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3AL8 Plexin A2 / Semaphorin 6A complex Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–570（552 aa） Fragment：sema and PSI domain (UNP RESIDUES 19-570)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.287
3AL8 Plexin A2 / Semaphorin 6A complex Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–570（552 aa） Fragment：sema and PSI domain (UNP RESIDUES 19-570)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.287
3OKW Mouse Semaphorin 6A, extracellular domains 1-2 Deposited 2010-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–571（553 aa）
Chain B 19–571（553 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CIT CITRIC ACID × 1 GOL GLYCEROL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；Polyethylene Glycol 3350 20% w/v, di-ammonium Hydrogen Citrate 200mM, 6% D-galactose, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.219

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

View Construct and Data Evidence
UniProt name SEM6A_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–556； UniProt 19–570 Author chain B； PDBConstruct 5–556； UniProt 19–570

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 3afc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3afc
Deposition date deposition_date2010-02-26
Structure title titleMouse Semaphorin 6A extracellular domain
Keywords keywordsBETA PROPELLER, Disulfide bond, Glycoprotein, Neurogenesis, IMMUNE RESPONSE, AXON GUIDANCE, MEMBRANE PROTEIN, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.99 Å
Radius of gyration Rg (electron density) rg_electron33.98 Å
Forward intensity I(0) i0216363000.00
Molecular weight molecular_weight117690.0 kDa
Excluded volume excluded_volume146970 ų
Envelope volume envelope_volume190570 ų
Hydration-shell volume shell_volume46431 ų
Envelope diameter envelope_diameter112.6 Å
Shell Rg shell_rg41.14 Å
Envelope Rg envelope_rg33.67 Å
Shape Rg shape_rg33.95 Å
Total Rg total_rg34.58 Å
Total atoms total_atoms8266
Residues n_residues1033
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 dmax111.2 Å
Rg (real space) rg_real34.91 Å
Rg uncertainty (real space) rg_real_error1.03 Å
I(0) (real space) i0_real2.1640e+08
I(0) uncertainty (real space) i0_real_error3.5590e+06
Rg (reciprocal space) rg_reciprocal34.96 Å
I(0) (reciprocal space) i0_reciprocal216400000.0000
Solution quality estimate total_estimate0.9071
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.0 Å
Skewness Skewness skewness0.214
Kurtosis Kurtosis kurtosis-0.605
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28430000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.949
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3afcA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3afcA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id3afcB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)