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3wsz

SorLA Vps10p domain in complex with Abeta-derived peptide

Method: X-RAY DIFFRACTION Dmax: 80.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sortilin-related receptor

Homo sapiens

UniProt Q92673

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 86–753 Fragment：N-terminal domain, UNP residues 86-753 10-mer peptide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；0.1M Tris, 1.41M Sodium Acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.20 Å R-free 0.296

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 3WSZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DM4 Solution structure of the second fn3 domain of human sorLA/LR11 Deposited 2006-04-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1651–1745（95 aa） Fragment：FN3
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 1.18mM uniformly 13C and 15N labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 10% D2O, 90% H2O | 10% D2O, 90% H2O
Resolution not provided
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2202–2214（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.70 Å R-free 0.226
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2202–2214（13 aa）
Not recorded HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.70 Å R-free 0.226
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2202–2214（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.00 Å R-free 0.233
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2202–2214（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) IOD IODIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.00 Å R-free 0.233
3WSX SorLA Vps10p domain in ligand-free form Deposited 2014-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–753（725 aa） Fragment：N-terminal domain, UNP residues 29-753
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PO4 PHOSPHATE ION × 4 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1M Sodium Acetate, 1.2M Sodium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.238
3WSY SorLA Vps10p domain in complex with its own propeptide fragment Deposited 2014-03-30 Different construct Different mutation/modification 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 86–753（668 aa） Fragment：N-terminal domain, UNP residues 86-753
Chain C 42–56（15 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M Cacodylate, 1.2M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.11 Å R-free 0.232
7VT0 Dimer structure of SORLA Deposited 2021-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 89–752（664 aa）
Chain B 89–752（664 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.40 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SORL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–669； UniProt 86–753

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 3wsz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3wsz
Deposition date deposition_date2014-03-30
Structure title titleSorLA Vps10p domain in complex with Abeta-derived peptide
Keywords keywordsBeta-Propeller, Receptor, PROTEIN BINDING; PROTEIN BINDING
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_guinier26.51 Å
Radius of gyration Rg (electron density) rg_electron25.25 Å
Forward intensity I(0) i068240900.00
Molecular weight molecular_weight64802.0 kDa
Excluded volume excluded_volume81096 ų
Envelope volume envelope_volume104120 ų
Hydration-shell volume shell_volume33457 ų
Envelope diameter envelope_diameter82.9 Å
Shell Rg shell_rg33.44 Å
Envelope Rg envelope_rg24.91 Å
Shape Rg shape_rg25.21 Å
Total Rg total_rg26.24 Å
Total atoms total_atoms4581
Residues n_residues568
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 dmax80.2 Å
Rg (real space) rg_real26.31 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real6.8240e+07
I(0) uncertainty (real space) i0_real_error1.0100e+06
Rg (reciprocal space) rg_reciprocal26.37 Å
I(0) (reciprocal space) i0_reciprocal68240000.0000
Solution quality estimate total_estimate0.9050
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.4 Å
Skewness Skewness skewness0.033
Kurtosis Kurtosis kurtosis-0.563
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13410000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)