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10rk

Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1

Method: ELECTRON MICROSCOPY Dmax: 225.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neuropilin-1

Mus musculus

UniProt P97333

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 Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count Chain E； UniProt 22–855 Chain F； UniProt 22–855 Chain K； UniProt 22–855 Chain L； UniProt 22–855 Not recorded Isoform VEGF-1 of Vascular endothelial growth factor A, long form × 4 （Q00731） Vascular endothelial growth factor receptor 2 × 4 （P35918） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CALCIUM ION × 8 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å

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 10RK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 22–855（834 aa）
Chain F 22–855（834 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.60 Å
10RJ Heparin-induced cis tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 22–855（834 aa）
Chain F 22–855（834 aa）
Chain K 22–855（834 aa）
Chain L 22–855（834 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.34 Å
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.223
4GZ9 Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) Deposited 2012-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 22–586（565 aa） Fragment：UNP RESIDUES 22-586
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES, pH 7.5, 1.5M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.70 Å R-free 0.223
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H 22–586（565 aa） Fragment：UNP RESIDUES 22-586
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 22–588（567 aa）
Chain F 22–588（567 aa）
Not recorded CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRP1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain E； PDBConstruct 4–837； UniProt 22–855 Author chain F； PDBConstruct 4–837； UniProt 22–855 Author chain K； PDBConstruct 4–837； UniProt 22–855 Author chain L； PDBConstruct 4–837； UniProt 22–855

Isoform VEGF-1 of Vascular endothelial growth factor A, long form

Mus musculus

UniProt Q00731

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 Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 27–190 Chain B； UniProt 27–190 Chain G； UniProt 27–190 Chain H； UniProt 27–190 Not recorded Neuropilin-1 × 4 （P97333） Vascular endothelial growth factor receptor 2 × 4 （P35918） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CALCIUM ION × 8 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å

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 10RK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 27–190（164 aa）
Chain B 27–190（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.60 Å
10RJ Heparin-induced cis tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 27–190（164 aa）
Chain B 27–190（164 aa）
Chain G 27–190（164 aa）
Chain H 27–190（164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.34 Å

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

View Construct and Data Evidence
UniProt name VEGFA_MOUSE
Isoform Q00731-2
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 12–175； UniProt 27–190 Author chain B； PDBConstruct 12–175； UniProt 27–190 Author chain G； PDBConstruct 12–175； UniProt 27–190 Author chain H； PDBConstruct 12–175； UniProt 27–190

Vascular endothelial growth factor receptor 2

Mus musculus

UniProt P35918

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 Heteromer Protein × 12 其他Polymer 4 PDB declaration: dodecameric（12） Consistent with protein copy count Chain C； UniProt 20–760 Chain D； UniProt 20–760 Chain I； UniProt 20–760 Chain J； UniProt 20–760 Not recorded Neuropilin-1 × 4 （P97333） Isoform VEGF-1 of Vascular endothelial growth factor A, long form × 4 （Q00731） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CALCIUM ION × 8 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.65 Å

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 10RK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10RI Dimeric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 20–760（741 aa）
Chain D 20–760（741 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.60 Å
10RJ Heparin-induced cis tetrameric complex of VEGF, VEGFR2 and Neuropilin 1 Deposited 2026-02-03 Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 20–760（741 aa）
Chain D 20–760（741 aa）
Chain I 20–760（741 aa）
Chain J 20–760（741 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.34 Å

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

View Construct and Data Evidence
UniProt name VGFR2_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 4–744； UniProt 20–760 Author chain D； PDBConstruct 4–744； UniProt 20–760 Author chain I； PDBConstruct 4–744； UniProt 20–760 Author chain J； PDBConstruct 4–744； UniProt 20–760

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 10rk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10rk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10rk
Deposition date deposition_date2026-02-03
Structure title titleHeparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1
Keywords keywordsVEGF, VEGFR, neuropilin, heparin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier85.24 Å
Radius of gyration Rg (electron density) rg_electron86.50 Å
Forward intensity I(0) i05034010000.00
Molecular weight molecular_weight591070.0 kDa
Excluded volume excluded_volume735710 ų
Envelope volume envelope_volume1428800 ų
Hydration-shell volume shell_volume153240 ų
Envelope diameter envelope_diameter358.3 Å
Shell Rg shell_rg71.47 Å
Envelope Rg envelope_rg84.94 Å
Shape Rg shape_rg86.52 Å
Total Rg total_rg86.17 Å
Total atoms total_atoms81918
Residues n_residues5196
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 dmax225.8 Å
Rg (real space) rg_real79.24 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real4.7870e+09
I(0) uncertainty (real space) i0_real_error8.9810e+07
Rg (reciprocal space) rg_reciprocal82.42 Å
I(0) (reciprocal space) i0_reciprocal4993000000.0000
Solution quality estimate total_estimate0.9198
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.8 Å
Skewness Skewness skewness0.309
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.0900 Å−1
Current regularization parameter α current_alpha0.6153
Highest regularization parameter α highest_alpha290600000.0000
Real-space data points n_real_points19
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.997; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.017
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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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8. Citations (1)

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9. Files and Curves (10)