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7vt0

Dimer structure of SORLA

Method: ELECTRON MICROSCOPY Dmax: 135.9 Å Quality: REASONABLE
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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 89–752 Chain B； UniProt 89–752 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen OTHER Resolution 3.40 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 7VT0 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification 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 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 ligand/ion Different experimental method 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
3WSZ SorLA Vps10p domain in complex with Abeta-derived peptide Deposited 2014-03-30 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 × 2 PDB declaration: dimeric
Chain A 86–753（668 aa） Fragment：N-terminal domain, UNP residues 86-753
Not recorded 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

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 1–664； UniProt 89–752 Author chain B； PDBConstruct 1–664； UniProt 89–752

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 7vt0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7vt0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7vt0
Deposition date deposition_date2021-10-27
Structure title titleDimer structure of SORLA
Keywords keywordsProtein sorting receptor, MEMBRANE PROTEIN; MEMBRANE 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_guinier43.59 Å
Radius of gyration Rg (electron density) rg_electron43.47 Å
Forward intensity I(0) i0337114000.00
Molecular weight molecular_weight149240.0 kDa
Excluded volume excluded_volume186040 ų
Envelope volume envelope_volume275910 ų
Hydration-shell volume shell_volume53991 ų
Envelope diameter envelope_diameter145.4 Å
Shell Rg shell_rg46.95 Å
Envelope Rg envelope_rg42.86 Å
Shape Rg shape_rg43.48 Å
Total Rg total_rg43.59 Å
Total atoms total_atoms10536
Residues n_residues1326
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 dmax135.9 Å
Rg (real space) rg_real43.73 Å
Rg uncertainty (real space) rg_real_error1.12 Å
I(0) (real space) i0_real3.3710e+08
I(0) uncertainty (real space) i0_real_error6.6830e+06
Rg (reciprocal space) rg_reciprocal43.59 Å
I(0) (reciprocal space) i0_reciprocal337100000.0000
Solution quality estimate total_estimate0.6197
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.3 Å
Skewness Skewness skewness0.360
Kurtosis Kurtosis kurtosis-0.603
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27250000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 0.979; Smooth: 0.194
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)