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5osi

Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)

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

Vacuolar protein sorting-associated protein 29

Homo sapiens

UniProt Q9UBQ0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） 1,2-ETHANEDIOL × 5 SODIUM ION × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1w24

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2r17 2r17 5gtu 5osh 5osh 5osh 5osh 5osi 5osi 5osi 5osi 5wyh

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VPS29_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–182； UniProt 1–182 Author chain D； PDBConstruct 1–182； UniProt 1–182 Author chain G； PDBConstruct 1–182； UniProt 1–182 Author chain J； PDBConstruct 1–182； UniProt 1–182

Vacuolar protein sorting-associated protein 35

Homo sapiens

UniProt Q96QK1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Interaptin × 1 （G8UZ99） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） 1,2-ETHANEDIOL × 5 SODIUM ION × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5f0k 5f0k 5f0k 5f0k 5f0k

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2r17 2r17 5f0j 5f0l 5f0m 5f0p 5osh 5osh 5osh 5osh 5osi 5osi

24 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VPS35_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–311； UniProt 471–781 Author chain E； PDBConstruct 1–311； UniProt 471–781 Author chain H； PDBConstruct 1–311； UniProt 471–781 Author chain K； PDBConstruct 1–311； UniProt 471–781

Interaptin

Legionella pneumophila subsp. pneumophila ATCC 43290

UniProt G8UZ99

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） 1,2-ETHANEDIOL × 2 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） 1,2-ETHANEDIOL × 2 SODIUM ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5oh5 5oh6 5oh6 5ot4 5ot4 5ot4 5ot4

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5osh 5osh 5osh 5osh 5osi 5osi 5osi 5wyh 5wyh

9 assemblies

View Construct and Data Evidence
UniProt name G8UZ99_LEGPN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–14； UniProt 163–176 Author chain F； PDBConstruct 1–14； UniProt 163–176 Author chain I； PDBConstruct 1–14； UniProt 163–176

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_id5osi
Deposition date deposition_date2017-08-17
Structure title titleStructure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
Keywords keywordsRetromer, Legionella pneumophila, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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.

5osi__assembly_1__model_1

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

Download this curve (.dat)

5osi__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5osi__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）24.27 Å
Rg (electron density)23.23 Å
Total Rg24.20 Å
Atom count3974
Residues493
Excluded volume71067 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5osi__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5osi__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5osi__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5osi__assembly_4__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 (6)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5osia_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.7 — YfcE-like
Domain ID domain_idd5osid_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.7 — YfcE-like
Domain ID domain_idd5osig_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.7 — YfcE-like
Domain ID domain_idd5osij_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.7 — YfcE-like

CATH v4.4 (8 domains)

Domain ID domain_id5osiA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id5osiB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C
Domain ID domain_id5osiD00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id5osiE00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C
Domain ID domain_id5osiG00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id5osiH00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C
Domain ID domain_id5osiJ00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id5osiK00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C
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7. Citations (1)