3DM7: Vps75 Histone Chaperone

Name: PDB 3DM7: Crystal Structure of the Vps75 Histone Chaperone
Published: 2008-09-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Crystal Structure of the Vps75 Histone Chaperone. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,795
Mol. weight: 55.6 kDa
Released: 9 Sept 2008

Explore 3DM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DM7 contains 24 α-helices and 12 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: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-51	40
α-helix	57-64	8
α-helix	68-71	4
α-helix	74-76	3
α-helix	77-80	4
β-strand	83-90	8	1
α-helix	91-93	3
β-strand	103-109	7	1
β-strand	112	1	2
β-strand	116	1	2
β-strand	119-128	10	1
β-strand	138-141	4	1
α-helix	150-155	6
α-helix	166-176	11
α-helix	179-182	4
α-helix	197-202	6
α-helix	203-208	6
α-helix	209-221	13

Chain B: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-51	39
α-helix	57-64	8
α-helix	68-70	3
α-helix	74-76	3
α-helix	77-80	4
β-strand	83-90	8	3
α-helix	91-93	3
β-strand	103-109	7	3
β-strand	112	1	4
β-strand	116	1	4
β-strand	119-128	10	3
β-strand	138-141	4	3
α-helix	150-155	6
α-helix	166-176	11
α-helix	179-182	4
α-helix	197-203	7
α-helix	204-208	5
α-helix	212-221	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 75	A, B	protein	234	Saccharomyces cerevisiae	P53853 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3DM7_1 Vacuolar protein sorting-associated protein 75 (chains A, B)
GSMMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFW
KIVLSQHVSFANYIRASDFKYMDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKE
QQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLMKDKRSPEGKKKYRQGMKT
IFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDEEGESGL

Primary citation

Structure of Vps75 and implications for histone chaperone function. Tang, Y., Meeth, K., Jiang, E. et al. Proc Natl Acad Sci U S A (2008) 105:12206-12211. DOI 10.1073/pnas.0802393105 · PubMed

Other PDB entries of the same protein (UniProt P53853 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZD7 1.85 Å, The structure of VPS75 (Vacuolar protein sorting-associated protein 75)
3C9D 2.0 Å, Crystal structure of Vps75
3C9B 2.42 Å, Crystal structure of SeMet Vps75
3Q66 2.71 Å, Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex…
3Q68 2.71 Å, Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex…
3Q33 2.8 Å, Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated…
3Q35 3.3 Å, Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated…
5AGC 4.0 Å, Crystallographic forms of the Vps75 tetramer
6O22 Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex…

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