6XS8: Chaetomium thermophilum Vps29

Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3. Determined by X-ray diffraction at 1.95 Å resolution. Released 14 Jul 2021.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Chaetomium thermophilum, synthetic construct
Chains: 2
Atoms: 1,755
Mol. weight: 23.96 kDa
Released: 14 Jul 2021

Explore 6XS8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XS8 contains 4 α-helices and 13 β-strands across 2 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.

Chain A: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	22-25	4
β-strand	35-39	5	1
α-helix	45-54	10
β-strand	58-61	4	1
β-strand	75-80	6	2
β-strand	83-88	6	2
α-helix	98-108	11
β-strand	112-115	4	2
β-strand	122-127	6	2
β-strand	130-135	6	2
α-helix	141-143	3
β-strand	156-163	8	1
β-strand	166-176	11	1
β-strand	182-192	11	1

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	3
β-strand	10	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A	protein	203	Chaetomium thermophilum	G0RZB5 (AlphaFold model)
48V-dty-gly-tyr-asp-pro-leu-gly-leu-lys-tyr-phe-ala	B	protein	13	synthetic construct

Sequence of entity 1 (A), FASTA

>6XS8_1 Vacuolar protein sorting-associated protein 29 (chains A)
GSMAFLILVIGNLHIPDRALDIPPKFKKLLSPGKISQTLCLGNLTDRATYDYLRSISPDL
KIVRGRMDVEATSLPLMQVVTHGSLRIGFLEGFTLVSEEPDVLLAEANKLDVDVLCWAGG
SHRFECFEYMDKFFVNPGSATGAFTTDWLAEGEEVVPSFCLMDVQGISLTLYVYQLRKDE
NGTENVAVEKVTYTKPVEPTGAS

Sequence of entity 2 (B), FASTA

>6XS8_2 48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA (chains B)
XYGYDPLGLKYFA

Primary citation

De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Chen, K.E., Guo, Q., Hill, T.A. et al. Sci Adv (2021) 7:eabg4007-eabg4007. DOI 10.1126/sciadv.abg4007 · PubMed

Other PDB entries of the same protein (UniProt G0RZB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W8M 1.52 Å, Crystal structure of Chaetomium thermophilum Vps29
7BLR 9.3 Å, Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex.
7BLP 9.5 Å, Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex
6H7W 11.4 Å, Model of retromer-Vps5 complex assembled on membrane.

Browse structure collections

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