5W8M: Chaetomium thermophilum Vps29

Crystal structure of Chaetomium thermophilum Vps29. Determined by X-ray diffraction at 1.52 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Chaetomium thermophilum
Chains: 6
Atoms: 10,397
Mol. weight: 134.66 kDa
Released: 13 Jun 2018

Explore 5W8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W8M contains 25 α-helices and 78 β-strands across 6 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
β-strand	13	1	2
α-helix	22-25	4
α-helix	26-28	3
β-strand	33-38	6	1
β-strand	43	1	2
α-helix	45-54	10
β-strand	58-60	3	1
β-strand	76-80	5	3
β-strand	83-88	6	3
α-helix	98-108	11
β-strand	112-115	4	3
β-strand	123-127	5	3
β-strand	130-134	5	3
β-strand	156-163	8	1
β-strand	166-176	11	1
β-strand	182-192	11	1

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	4
β-strand	13	1	5
α-helix	22-27	6
β-strand	35-38	4	4
β-strand	43	1	5
α-helix	45-54	10
β-strand	58-60	3	4
β-strand	75-80	6	1
β-strand	83-88	6	1
α-helix	98-108	11
β-strand	112-114	3	1
β-strand	122-127	6	1
β-strand	130-135	6	1
β-strand	156-163	8	4
β-strand	166-176	11	4
β-strand	182-192	11	4

Chain C: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	13	1	7
α-helix	22-27	6
β-strand	35-38	4	6
β-strand	43	1	7
α-helix	45-54	10
β-strand	58-60	3	6
β-strand	75-80	6	8
β-strand	83-88	6	8
α-helix	98-108	11
β-strand	112-114	3	8
β-strand	122-127	6	8
β-strand	130-135	6	8
α-helix	141-143	3
α-helix	151-155	5
β-strand	156-163	8	6
β-strand	166-175	10	6
β-strand	183-192	10	6

Chain D: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	9
β-strand	13	1	10
α-helix	22-25	4
α-helix	26-28	3
β-strand	33-38	6	9
β-strand	43	1	10
α-helix	45-54	10
β-strand	58-60	3	9
β-strand	76-80	5	11
β-strand	83-88	6	11
α-helix	98-108	11
β-strand	112-115	4	11
β-strand	122-127	6	11
β-strand	130-135	6	11
α-helix	141-143	3
β-strand	156-163	8	9
β-strand	166-176	11	9
β-strand	182-192	11	9

Chain E: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	12
β-strand	13	1	13
α-helix	22-25	4
β-strand	33-38	6	12
β-strand	43	1	13
α-helix	45-54	10
β-strand	58-60	3	12
β-strand	75-80	6	14
β-strand	83-88	6	14
α-helix	98-108	11
β-strand	112-114	3	14
β-strand	122-127	6	14
β-strand	130-135	6	14
α-helix	141-143	3
α-helix	153-155	3
β-strand	156-163	8	12
β-strand	166-176	11	12
β-strand	182-192	11	12

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	11
β-strand	13	1	15
α-helix	22-27	6
β-strand	35-38	4	11
β-strand	43	1	15
α-helix	45-54	10
β-strand	58-60	3	11
β-strand	75-80	6	12
β-strand	83-88	6	12
α-helix	98-108	11
β-strand	112-114	3	12
β-strand	123-127	5	12
β-strand	130-134	5	12
β-strand	156-163	8	11
β-strand	166-176	11	11
β-strand	182-192	11	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, B, C, D, E, F	protein	203	Chaetomium thermophilum	G0RZB5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5W8M_1 Vacuolar protein sorting-associated protein 29 (chains A, B, C, D, E, F)
GSMAFLILVIGNLHIPDRALDIPPKFKKLLSPGKISQTLCLGNLTDRATYDYLRSISPDL
KIVRGRMDVEATSLPLMQVVTHGSLRIGFLEGFTLVSEEPDVLLAEANKLDVDVLCWAGG
SHRFECFEYMDKFFVNPGSATGAFTTDWLAEGEEVVPSFCLMDVQGISLTLYVYQLRKDE
NGTENVAVEKVTYTKPVEPTGAS

Primary citation

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Kovtun, O., Leneva, N., Bykov, Y.S. et al. Nature (2018) 561:561-564. DOI 10.1038/s41586-018-0526-z · PubMed

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

6XS8 1.95 Å, Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic…
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.

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