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1q47

Structure of the Semaphorin 3A Receptor-Binding Module

Method: X-RAY DIFFRACTION Dmax: 112.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Semaphorin 3A

Mus musculus

UniProt O08665

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–520 Chain B； UniProt 26–520 Fragment：Sema-3A 65k (residues 26-520) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Tris, PEG 8000, heptyl-beta-D thioglucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.80 Å R-free 0.294

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 1Q47 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GZ8 Mouse Semaphorin 3A, domains Sema-PSI-IG Deposited 2012-09-06 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 21–569（549 aa） Fragment：UNP RESIDUES 21-675
Chain B 21–569（549 aa） Fragment：UNP RESIDUES 21-675
Not recorded CA CALCIUM ION × 5 ACT ACETATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M sodium cacodylate, 0.1M calcium acetate, 12% w/v PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.30 Å R-free 0.265
4GZA Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 Deposited 2012-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 21–555（535 aa） Fragment：UNP RESIDUES 21-555
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 1% v/v ethyl acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；70mM HEPES, pH 7.5, 1.4% w/v PEG 400, 12% v/v glycerol, 1.4M ammonium sulphate, 8% v/v acetonitrile , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 7.00 Å R-free 0.285
7M0R Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex Deposited 2021-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 21–569（549 aa）
Chain D 21–569（549 aa）
Mutation：A106K,551ARTRA555,731AAQAA735,758ANRA761 Mutation：A106K,551ARTRA555,731AAQAA735,758ANRA761 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

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

View Construct and Data Evidence
UniProt name SEM3A_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–495； UniProt 26–520 Author chain B； PDBConstruct 1–495； UniProt 26–520

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 1q47

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q47
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1q47
Deposition date deposition_date2003-08-01
Structure title titleStructure of the Semaphorin 3A Receptor-Binding Module
Keywords keywordsbeta propeller, 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_guinier34.98 Å
Radius of gyration Rg (electron density) rg_electron34.37 Å
Forward intensity I(0) i0196194000.00
Molecular weight molecular_weight112290.0 kDa
Excluded volume excluded_volume140190 ų
Envelope volume envelope_volume181670 ų
Hydration-shell volume shell_volume44255 ų
Envelope diameter envelope_diameter117.0 Å
Shell Rg shell_rg40.92 Å
Envelope Rg envelope_rg33.93 Å
Shape Rg shape_rg34.39 Å
Total Rg total_rg34.80 Å
Total atoms total_atoms7923
Residues n_residues979
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 dmax112.8 Å
Rg (real space) rg_real35.00 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real1.9620e+08
I(0) uncertainty (real space) i0_real_error3.2680e+06
Rg (reciprocal space) rg_reciprocal34.99 Å
I(0) (reciprocal space) i0_reciprocal196200000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.6 Å
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.578
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32330000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.906
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1q47a_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.12 — Sema domain
Family Family familyb.69.12.1 — Sema domain
Domain ID domain_idd1q47b_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.12 — Sema domain
Family Family familyb.69.12.1 — Sema domain

CATH v4.4 (2 domains)

Domain ID domain_id1q47A00
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_id1q47B00
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)