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9o9i

Crystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Vacuolar protein sorting-associated protein 29

Mus musculus

UniProt Q9QZ88

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU × 1 （Q5VZ89） CACODYLATE ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1z2w 1z2w 1z2x 1z2x 3psn 3psn 3pso 3pso

8 assemblies

Homodimer
1z2w 1z2x 3psn 3pso

4 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6tl0 6vab 6vac 7u6f 8fud 8fud 8tta 8tta 8ttc 8ttc 8ttd 9o9i

12 assemblies

View Construct and Data Evidence
UniProt name VPS29_MOUSE
Isoform Q9QZ88-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–188； UniProt 2–186

ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU

OrganismNot specified

UniProt Q5VZ89

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Isoform 2 of Vacuolar protein sorting-associated protein 29 × 1 （Q9QZ88） CACODYLATE ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
9o9i

1 assemblies

View Construct and Data Evidence
UniProt name DEN4C_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–18； UniProt 1189–1206

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id9o9i
Deposition date deposition_date2025-04-18
Last revision last_revision2025-08-13
Structure title titleCrystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)
Keywords keywordsRetromer, endosome, membrane trafficking, Protein transport, DENN domain; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9o9i__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9o9i__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9o9i__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）17.07 Å
Rg (electron density)15.71 Å
Total Rg16.90 Å
Atom count1582
Residues199
Excluded volume28383 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9o9i__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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7. Citations (1)