8RKS: VPS29-VPS35
Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Determined by X-ray diffraction at 3.1 Å resolution. Released 24 Apr 2024.
- Method
- X-ray diffraction
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 15,571
- Mol. weight
- 228.63 kDa
- Released
- 24 Apr 2024
Explore 8RKS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8RKS contains 79 α-helices and 58 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A and C: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 1 |
| α-helix | 20-25 | 6 | |
| β-strand | 33-36 | 4 | 1 |
| α-helix | 43-50 | 8 | |
| β-strand | 55-58 | 4 | 1 |
| β-strand | 72-77 | 6 | 2 |
| β-strand | 80-85 | 6 | 2 |
| α-helix | 96-106 | 11 | |
| β-strand | 110-112 | 3 | 2 |
| β-strand | 120-124 | 5 | 2 |
| β-strand | 127-131 | 5 | 2 |
| β-strand | 140 | 1 | 3 |
| β-strand | 143 | 1 | 3 |
| β-strand | 149-156 | 8 | 1 |
| β-strand | 159-168 | 10 | 1 |
| β-strand | 171-180 | 10 | 1 |
Chain B: 16 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 483-496 | 14 | |
| α-helix | 503-517 | 15 | |
| α-helix | 522-525 | 4 | |
| α-helix | 529-545 | 17 | |
| α-helix | 553-573 | 21 | |
| α-helix | 578-594 | 17 | |
| α-helix | 599-617 | 19 | |
| α-helix | 621-637 | 17 | |
| α-helix | 643-657 | 15 | |
| α-helix | 663-672 | 10 | |
| α-helix | 674-679 | 6 | |
| β-strand | 681 | 1 | 4 |
| β-strand | 689 | 1 | 4 |
| α-helix | 693-708 | 16 | |
| α-helix | 713-732 | 20 | |
| α-helix | 740-753 | 14 | |
| α-helix | 754-756 | 3 | |
| α-helix | 761-777 | 17 | |
Chain D: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 483-485 | 3 | |
| α-helix | 486-498 | 13 | |
| α-helix | 503-517 | 15 | |
| α-helix | 518-520 | 3 | |
| α-helix | 525-545 | 21 | |
| α-helix | 553-573 | 21 | |
| α-helix | 578-594 | 17 | |
| α-helix | 599-617 | 19 | |
| α-helix | 621-637 | 17 | |
| α-helix | 643-657 | 15 | |
| α-helix | 663-672 | 10 | |
| α-helix | 674-678 | 5 | |
| β-strand | 681 | 1 | 8 |
| β-strand | 689 | 1 | 8 |
| α-helix | 693-708 | 16 | |
| α-helix | 713-732 | 20 | |
| α-helix | 740-753 | 14 | |
| α-helix | 754-756 | 3 | |
| α-helix | 761-776 | 16 | |
Chain E: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 9 |
| α-helix | 20-25 | 6 | |
| β-strand | 33-36 | 4 | 9 |
| α-helix | 43-50 | 8 | |
| β-strand | 55-58 | 4 | 9 |
| α-helix | 59-61 | 3 | |
| β-strand | 72-77 | 6 | 10 |
| β-strand | 80-85 | 6 | 10 |
| α-helix | 96-106 | 11 | |
| β-strand | 110-112 | 3 | 10 |
| β-strand | 119-124 | 6 | 10 |
| β-strand | 127-132 | 6 | 10 |
| β-strand | 149-156 | 8 | 9 |
| β-strand | 159-168 | 10 | 9 |
| β-strand | 171-180 | 10 | 9 |
Chain F: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 484-498 | 15 | |
| α-helix | 503-517 | 15 | |
| α-helix | 518-520 | 3 | |
| α-helix | 521-545 | 25 | |
| α-helix | 553-573 | 21 | |
| α-helix | 578-594 | 17 | |
| α-helix | 599-617 | 19 | |
| α-helix | 621-637 | 17 | |
| α-helix | 643-657 | 15 | |
| α-helix | 663-672 | 10 | |
| α-helix | 674-678 | 5 | |
| β-strand | 681 | 1 | 11 |
| β-strand | 689 | 1 | 11 |
| α-helix | 693-708 | 16 | |
| α-helix | 713-732 | 20 | |
| α-helix | 740-753 | 14 | |
| α-helix | 761-778 | 18 | |
Chain G: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 12 |
| α-helix | 20-25 | 6 | |
| β-strand | 33-36 | 4 | 12 |
| α-helix | 43-50 | 8 | |
| β-strand | 55-58 | 4 | 12 |
| β-strand | 72-77 | 6 | 13 |
| β-strand | 80-85 | 6 | 13 |
| α-helix | 96-106 | 11 | |
| β-strand | 110-112 | 3 | 13 |
| β-strand | 120-124 | 5 | 13 |
| β-strand | 127-131 | 5 | 13 |
| β-strand | 140 | 1 | 14 |
| β-strand | 143 | 1 | 14 |
| α-helix | 146-148 | 3 | |
| β-strand | 149-156 | 8 | 12 |
| β-strand | 159-168 | 10 | 12 |
| β-strand | 171-180 | 10 | 12 |
Chain H: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 486-495 | 10 | |
| α-helix | 498-500 | 3 | |
| α-helix | 503-517 | 15 | |
| α-helix | 518-520 | 3 | |
| α-helix | 522-545 | 24 | |
| α-helix | 553-573 | 21 | |
| α-helix | 578-594 | 17 | |
| α-helix | 599-617 | 19 | |
| α-helix | 621-637 | 17 | |
| α-helix | 643-657 | 15 | |
| α-helix | 663-672 | 10 | |
| α-helix | 674-678 | 5 | |
| β-strand | 681 | 1 | 15 |
| β-strand | 689 | 1 | 15 |
| α-helix | 693-708 | 16 | |
| α-helix | 713-732 | 20 | |
| α-helix | 740-753 | 14 | |
| α-helix | 754-756 | 3 | |
| α-helix | 761-778 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vacuolar protein sorting-associated protein 29 | A, C, E, G | protein | 182 | Homo sapiens | Q9UBQ0 (AlphaFold model) |
| Vacuolar protein sorting-associated protein 35 | B, D, F, H | protein | 311 | Homo sapiens | Q96QK1 (AlphaFold model) |
| WASH complex subunit 2A | I, J, K, L | protein | 7 | Homo sapiens | Q641Q2 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>8RKS_1 Vacuolar protein sorting-associated protein 29 (chains A, C, E, G)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KP
Sequence of entity 2 (B, D, F, H), FASTA
>8RKS_2 Vacuolar protein sorting-associated protein 35 (chains B, D, F, H)
QPDQPVEDPDPEDFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLP
PLVFAAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALA
AGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLR
TQCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQC
MDPSLQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHF
HNTLEHLRLRR
Sequence of entity 3 (I, J, K, L), FASTA
>8RKS_3 WASH complex subunit 2A (chains I, J, K, L)
DDPLNAF
Primary citation
Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21. Romano-Moreno, M., Astorga-Simon, E.N., Rojas, A.L. et al. Protein Sci (2024) 33:e4980-e4980. DOI 10.1002/pro.4980 · PubMed
Other PDB entries of the same protein (UniProt Q9UBQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8ESE 1.35 Å, Crystal structure of human Vps29 bound to a peptide from Vps35L
- 5GTU 1.5 Å, Structural and mechanistic insights into regulation of the retromer coat by TBC1d5
- 6XS7 1.58 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2
- 6XSA 1.83 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2
- 6XS5 2.01 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
- 1W24 2.1 Å, Crystal Structure Of human Vps29
- 8R0J 2.4 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
- 5WYH 2.46 Å, Crystal structure of RidL(1-200) complexed with VPS29
- 8R02 2.5 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
- 5OSI 2.52 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
- 6XS9 2.69 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1
- 2R17 2.8 Å, Functional architecture of the retromer cargo-recognition complex
Browse structure collections
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