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4gz8

Mouse Semaphorin 3A, domains Sema-PSI-IG

Method: X-RAY DIFFRACTION Dmax: 114.1 Å Quality: EXCELLENT
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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 Other combination Homooligomer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 21–569 Chain B； UniProt 21–569 Fragment：UNP RESIDUES 21-675 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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

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 4GZ8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Q47 Structure of the Semaphorin 3A Receptor-Binding Module Deposited 2003-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–520（495 aa） Fragment：Sema-3A 65k (residues 26-520)
Chain B 26–520（495 aa） Fragment：Sema-3A 65k (residues 26-520)
Not recorded 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
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 4–552； UniProt 21–569 Author chain B； PDBConstruct 4–552； UniProt 21–569

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 4gz8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gz8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gz8
Deposition date deposition_date2012-09-06
Structure title titleMouse Semaphorin 3A, domains Sema-PSI-IG
Keywords keywordssema, multi-domain, cell-cell signaling, plexin, glycosilated, extracellular, 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_guinier36.24 Å
Radius of gyration Rg (electron density) rg_electron35.37 Å
Forward intensity I(0) i0252762000.00
Molecular weight molecular_weight126260.0 kDa
Excluded volume excluded_volume156840 ų
Envelope volume envelope_volume207420 ų
Hydration-shell volume shell_volume48133 ų
Envelope diameter envelope_diameter116.1 Å
Shell Rg shell_rg42.52 Å
Envelope Rg envelope_rg35.03 Å
Shape Rg shape_rg35.39 Å
Total Rg total_rg35.81 Å
Total atoms total_atoms8886
Residues n_residues1112
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 dmax114.1 Å
Rg (real space) rg_real36.14 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real2.5280e+08
I(0) uncertainty (real space) i0_real_error4.3380e+06
Rg (reciprocal space) rg_reciprocal36.21 Å
I(0) (reciprocal space) i0_reciprocal252800000.0000
Solution quality estimate total_estimate0.9073
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.5 Å
Skewness Skewness skewness0.177
Kurtosis Kurtosis kurtosis-0.641
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35020000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.913
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4gz8A01
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_id4gz8A02
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_id4gz8B01
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_id4gz8B02
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
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8. Citations (1)

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9. Files and Curves (10)