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2fau

Crystal structure of human vps26

Method: X-RAY DIFFRACTION Dmax: 94.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar protein sorting 26

Homo sapiens

UniProt O75436

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–327 Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；8% PEG 8000 100mM Na cacodylate pH 6.5 15% glycerol 10mM DTT 1mM TmCl3, VAPOR DIFFUSION, SITTING DROP, temperature 300K Resolution 2.10 Å R-free 0.284

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 2FAU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 Deposited 2015-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–326（325 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.9 M AmSO4, 0.1 M MES pH 6.0
Resolution 2.70 Å R-free 0.246
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–317（317 aa）
Not recorded SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol
Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–321（320 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol
Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–321（321 aa） Fragment：Residues 1-321
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol
Resolution 2.78 Å R-free 0.261
7BLO VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins Deposited 2021-01-18 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 × 8 PDB declaration: octameric
Chain F 8–301（294 aa）
Chain J 8–301（294 aa）
Not recorded PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å

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

View Construct and Data Evidence
UniProt name VPS26_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–329； UniProt 1–327

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 2fau

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2fau
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2fau
Deposition date deposition_date2005-12-08
Structure title titleCrystal structure of human vps26
Keywords keywordsARRESTIN, RETROMER, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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_guinier25.90 Å
Radius of gyration Rg (electron density) rg_electron25.54 Å
Forward intensity I(0) i018670600.00
Molecular weight molecular_weight33994.0 kDa
Excluded volume excluded_volume43088 ų
Envelope volume envelope_volume53965 ų
Hydration-shell volume shell_volume19945 ų
Envelope diameter envelope_diameter94.8 Å
Shell Rg shell_rg29.43 Å
Envelope Rg envelope_rg25.78 Å
Shape Rg shape_rg25.45 Å
Total Rg total_rg26.32 Å
Total atoms total_atoms2389
Residues n_residues286
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 dmax94.3 Å
Rg (real space) rg_real26.25 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real1.8670e+07
I(0) uncertainty (real space) i0_real_error2.7060e+05
Rg (reciprocal space) rg_reciprocal26.14 Å
I(0) (reciprocal space) i0_reciprocal18670000.0000
Solution quality estimate total_estimate0.7857
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.6 Å
Skewness Skewness skewness0.667
Kurtosis Kurtosis kurtosis-0.050
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6108000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.579; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.494; Smooth: 0.981
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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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2fauA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640 —
Domain ID domain_id2fauA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640 —
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8. Citations (1)

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9. Files and Curves (10)