5ZBA: Rtt109-Asf1-H3-H4-CoA complex

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex. Determined by X-ray diffraction at 3.5 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 5,534
Mol. weight: 113.03 kDa
Ligands: COA
Released: 25 Jul 2018

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

Secondary structure: helices and β-sheets

5ZBA contains 28 α-helices and 30 β-strands across 4 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
β-strand	17	1	1
β-strand	21-29	9	2
β-strand	32-34	3	2
α-helix	39-41	3
α-helix	46-48	3
β-strand	49-60	12	2
β-strand	70-81	12	2
β-strand	85-95	11	2
α-helix	98-101	4
α-helix	110-125	16
β-strand	132-139	8	2
α-helix	150-152	3
α-helix	161-177	17
β-strand	180	1	2
β-strand	201-207	7	2
α-helix	213-217	5
α-helix	222-226	5
β-strand	234-235	2	2
α-helix	240-243	4
α-helix	251-253	3
α-helix	262-271	10
α-helix	296-303	8
β-strand	316-323	8	2
β-strand	415-418	4	2
α-helix	420-431	12
α-helix	438-455	18
β-strand	463-466	4	2
β-strand	469	1	1

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	3
β-strand	17	1	4
α-helix	21	1
β-strand	22-30	9	3
β-strand	38-45	8	4
β-strand	54-62	9	4
β-strand	68-76	9	3
α-helix	77-80	4
α-helix	81-83	3
β-strand	92-101	10	4
β-strand	104-117	14	4
α-helix	120-124	5
α-helix	132-134	3
β-strand	135-139	5	4
β-strand	145-148	4	4

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	5
α-helix	48-50	3
α-helix	64-77	14
β-strand	83-84	2	6
α-helix	86-112	27
β-strand	118-119	2	5
α-helix	121-131	11

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	5
α-helix	51-75	25
β-strand	80-81	2	6
α-helix	83-90	8
β-strand	95-98	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage response protein Rtt109, putative	A	protein	544	Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)	Q4WUS9 (AlphaFold model)
Histone chaperone asf1	B	protein	188	Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)	Q4WXX5 (AlphaFold model)
Histone H3	C	protein	136	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P61830 (AlphaFold model)
Histone H4	D	protein	103	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02309 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5ZBA_1 DNA damage response protein Rtt109, putative (chains A)
SMSKVDVDLGDSLAKVLPTGVKVTIRHISSAPSPCVALFAAPPGEEPESTFCENHFLAVS
ISPNENEESEVIIFGIEVLVYGTAHLTTIFVSKADSTGYLHLLKNAPKVSLLRLISNAFL
SFLVQTHQRPGVRLMVSLFARAQNQYLFPGSIENPEKHVLDDRGLIKWWCRVIDPILREY
EPETGSHEKAVDDQTQESAKSSATAFLIVPGCDKFETRGFFPITARSDGKDRPRWLNSYP
LHQLCDNPNAPPRCLVPRFPDDPKTRFLIDLDDELPESTGAAGSKENSGHWRSVKSLAQF
WEMMSFRQECSAGRLVGFLWLVINPPGLVNSVQMTSSRVASRDVENVLSESAKTTHDATK
QKDEAASVSSPPHPSTSGLQTSPIALPGVSSSDTHATVQQATGPSAFFWPDTGRGHAVLS
EEDYKAAINFLIDQDFNTKHKAIASTKAWAEKVASLADQLWVGQRVEGRNATTEPGQKHT
DATTVINTAFVRKRKTADEESDKPGEVRGAPGDSEEVNPTPVQSNQAPSVNVLNANLLRK
KKKT

Sequence of entity 2 (B), FASTA

>5ZBA_2 Histone chaperone asf1 (chains B)
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSVVSLLGVKIVNNPAPFLAPYQFEI
TFECLEQLQKDLEWKLTYVGSATSSEYDQELDSLLVGPIPVGVNKFLFEADAPDLKRIPT
SEILGVTVILLTCSYDGREFVRVGYYVNNEYDSEELTQDPPAKPIIERIRRNILAEKPRV
TRFAIKWD

Sequence of entity 3 (C), FASTA

>5ZBA_3 Histone H3 (chains C)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS

Sequence of entity 4 (D), FASTA

>5ZBA_4 Histone H4 (chains D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Ligands and cofactors

ID	Name	Formula	Copies
COA	Coenzyme a	C21 H36 N7 O16 P3 S	1

Water and common crystallization additives (IOD) are not listed.

Primary citation

Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109. Zhang, L., Serra-Cardona, A., Zhou, H. et al. Cell (2018) 174:818-830.e11. DOI 10.1016/j.cell.2018.07.005 · PubMed

Other PDB entries of the same protein (UniProt Q4WUS9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ZB9 2.5 Å, Crystal structure of Rtt109 from Aspergillus fumigatus
5ZBB 3.6 Å, Crystal structure of Rtt109-Asf1-H3-H4 complex

Browse structure collections

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