1w7p

The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36)

Method: X-RAY DIFFRACTION Dmax: 127.0 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

VPS22, YPL002C

SACCHAROMYCES CEREVISIAE

UniProt Q12483

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–233 Not recorded VPS25, YJR102C × 2 (P47142) VPS36P, YLR417W × 1 (Q06696) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL Resolution 3.60 Å R-free 0.330

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SNF8_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–233; UniProt 1–233

VPS25, YJR102C

SACCHAROMYCES CEREVISIAE

UniProt P47142

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–202 Chain C; UniProt 1–202 Not recorded VPS22, YPL002C × 1 (Q12483) VPS36P, YLR417W × 1 (Q06696) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL Resolution 3.60 Å R-free 0.330

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YJ72_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–202; UniProt 1–202 Author chain C; PDBConstruct 1–202; UniProt 1–202

VPS36P, YLR417W

SACCHAROMYCES CEREVISIAE

UniProt Q06696

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–566 Not recorded VPS22, YPL002C × 1 (Q12483) VPS25, YJR102C × 2 (P47142) X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL Resolution 3.60 Å R-free 0.330

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.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VPS36_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–566; UniProt 1–566

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 1w7p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w7p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w7p
Deposition date deposition_date2004-09-07
Structure title titleThe crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36)
Keywords keywordsESCRT-II COMPLEX, ENDOSOMAL PROTEIN SORTING, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.14
Radius of gyration Rg (electron density) rg_electron36.03
Forward intensity I(0) i0115265000.00
Molecular weight molecular_weight87269.0 kDa
Excluded volume excluded_volume109890 ų
Envelope volume envelope_volume155640 ų
Hydration-shell volume shell_volume38720 ų
Envelope diameter envelope_diameter130.4
Shell Rg shell_rg38.73
Envelope Rg envelope_rg37.00
Shape Rg shape_rg36.03
Total Rg total_rg36.24
Total atoms total_atoms6134
Residues n_residues748
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.0
Rg (real space) rg_real36.35
Rg uncertainty (real space) rg_real_error1.33
I(0) (real space) i0_real1.1530e+08
I(0) uncertainty (real space) i0_real_error1.8390e+06
Rg (reciprocal space) rg_reciprocal36.22
I(0) (reciprocal space) i0_reciprocal115300000.0000
Solution quality estimate total_estimate0.8526
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.3
Skewness Skewness skewness0.472
Kurtosis Kurtosis kurtosis-0.232
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22390000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.835; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1w7pa1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pa2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pb1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pb2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pc1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pc2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pd1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain
Domain ID domain_idd1w7pd2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.54 — Vacuolar sorting protein domain

CATH v4.4 (9 domains)

Domain ID domain_id1w7pA01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily180
Domain ID domain_id1w7pA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1w7pA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1w7pB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily570 — "Winged helix" DNA-binding domain. Chain C. Domain 1
Domain ID domain_id1w7pB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1w7pC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily570 — "Winged helix" DNA-binding domain. Chain C. Domain 1
Domain ID domain_id1w7pC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1w7pD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1w7pD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

8. Citations (2)

9. Files and Curves (10)