6O22: Vacuolar protein sorting-associated protein 75

Name: PDB 6O22: Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate.
Published: 2019-07-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate. Determined by solution NMR. Released 31 Jul 2019.

Method: Solution NMR
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Xenopus laevis
Chains: 6
Atoms: 9,731
Mol. weight: 170.48 kDa
Released: 31 Jul 2019

Explore 6O22 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O22 contains 57 α-helices and 52 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: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-51	42
α-helix	57-64	8
α-helix	66-71	6
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	119-127	9	1
β-strand	139-141	3	1
α-helix	150-152	3
α-helix	166-176	11
α-helix	181-184	4
α-helix	197-203	7
α-helix	204-208	5
α-helix	212-219	8

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-39	29
α-helix	41-51	11
α-helix	58-61	4
α-helix	68-70	3
α-helix	77-80	4
β-strand	83-89	7	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	131	1	5
β-strand	133	1	5
β-strand	138-141	4	3
α-helix	150-152	3
α-helix	157-159	3
α-helix	168-176	9
α-helix	179-183	5
α-helix	197-202	6
α-helix	203-207	5
α-helix	212-220	9

Chain C: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	12	1	6
β-strand	16-23	8	7
α-helix	24-26	3
β-strand	27-29	3	7
α-helix	34-36	3
β-strand	45-56	12	7
β-strand	61-73	13	7
β-strand	79-90	12	7
α-helix	100-113	14
β-strand	114	1	8
α-helix	116-119	4
β-strand	123	1	9
β-strand	124	1	7
α-helix	136-137	2
β-strand	142	1	5
α-helix	144-158	15
α-helix	165-167	3
α-helix	169-175	7
β-strand	177	1	9
β-strand	186-193	8	7
α-helix	195-197	3
α-helix	204-206	3
α-helix	215-230	16
β-strand	234	1	10
β-strand	239-243	5	7
α-helix	249-255	7
α-helix	256-258	3
β-strand	264-266	3	7
β-strand	277	1	11
α-helix	278-280	3
α-helix	289-299	11
β-strand	307	1	11
α-helix	308-317	10
α-helix	319-321	3
β-strand	328-334	7	7
β-strand	336	1	10
β-strand	342	1	8
β-strand	350	1	7
α-helix	355-366	12
α-helix	373-391	19
α-helix	394-395	2
β-strand	396-399	4	7
β-strand	402	1	6

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	12
β-strand	16-17	2	13
β-strand	22-30	9	12
β-strand	38-44	7	13
α-helix	51-53	3
β-strand	55-62	8	13
α-helix	65-66	2
β-strand	68-76	9	12
α-helix	77-79	3
α-helix	86-89	4
β-strand	93-101	9	13
β-strand	104-117	14	13
α-helix	120-124	5
β-strand	135-139	5	13
β-strand	145-148	4	13

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
β-strand	83-84	2	14
α-helix	86-113	28
β-strand	118-119	2	15
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	31-40	10
β-strand	45-46	2	15
α-helix	50-75	26
β-strand	80-81	2	14
α-helix	83-89	7
β-strand	95-97	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 75	A, B	protein	264	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53853 (AlphaFold model)
Histone acetyltransferase RTT109	C	protein	442	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q07794 (AlphaFold model)
Histone chaperone ASF1	D	protein	279	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32447 (AlphaFold model)
Histone H3.2	E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	F	protein	103	Xenopus laevis	P62799

Sequence of entity 1 (A, B), FASTA

>6O22_1 Vacuolar protein sorting-associated protein 75 (chains A, B)
MMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKI
VLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQ
VTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIF
GWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDEEGESGLSADGDSED
DDGSLGEVDLPLSDEEPSSKKRKV

Sequence of entity 2 (C), FASTA

>6O22_2 Histone acetyltransferase RTT109 (chains C)
GMDPNSMSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFS
LFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSI
DPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQD
LYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECF
QNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFI
HQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKS
RKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPAS
NINTLAITMLKPRKKAKALPKT

Sequence of entity 3 (D), FASTA

>6O22_3 Histone chaperone ASF1 (chains D)
SSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSI
LVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEE
ELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGVDDEEEEDDEEE
DDDEDDEDDEDDDQEDGEGEAEEAAEEEEEEEEKTEDNETNLEEEEEDIENSDGDEEEGE
EEVGSVDKNEDGNDKKRRKIEGGSTDIESTPKDAARSTN

Sequence of entity 4 (E), FASTA

>6O22_4 Histone H3.2 (chains E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 5 (F), FASTA

>6O22_5 Histone H4 (chains F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Primary citation

Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Danilenko, N., Lercher, L., Kirkpatrick, J. et al. Nat Commun (2019) 10:3435-3435. DOI 10.1038/s41467-019-11410-7 · 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
3DM7 2.0 Å, Crystal Structure of the Vps75 Histone Chaperone
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

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