8DEI: Cac1 KER domain

Structure of the Cac1 KER domain. Determined by X-ray diffraction at 2.81 Å resolution. Released 5 Jul 2023.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Escherichia coli, Saccharomyces cerevisiae
Chains: 4
Atoms: 14,713
Mol. weight: 223.15 kDa
Ligands: PO4
Released: 5 Jul 2023

Explore 8DEI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DEI contains 97 α-helices and 93 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: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
α-helix	17-31	15
β-strand	34-38	5	1
α-helix	43-50	8
α-helix	51-53	3
β-strand	59-63	5	1
α-helix	64-73	10
β-strand	76	1	2
α-helix	77-79	3
α-helix	83-88	6
β-strand	89	1	3
α-helix	91-95	5
β-strand	98-99	2	4
β-strand	102-103	2	4
β-strand	106-111	6	1
β-strand	114-118	5	5
β-strand	128	1	6
α-helix	129-131	3
α-helix	132-141	10
β-strand	145-147	3	5
α-helix	154-161	8
β-strand	167-172	6	7
β-strand	175-182	8	7
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	5
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	5
α-helix	246-248	3
β-strand	249-250	2	6
β-strand	253-254	2	6
α-helix	255	1
α-helix	257	1
β-strand	258-259	2	8
β-strand	260-266	7	1
β-strand	267	1	2
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	1
β-strand	304	1	3
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	8
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-367	11
α-helix	372-385	14
α-helix	387-474	88

Chain B: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	9
α-helix	17-31	15
β-strand	34-38	5	9
α-helix	43-50	8
α-helix	51-53	3
β-strand	59-63	5	9
α-helix	64-73	10
β-strand	76	1	10
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	11
α-helix	91-95	5
β-strand	98-99	2	12
β-strand	102-103	2	12
β-strand	106-111	6	9
β-strand	114-118	5	13
β-strand	128	1	14
α-helix	131-141	11
β-strand	145-147	3	13
α-helix	154-161	8
β-strand	167-171	5	15
β-strand	176-182	7	15
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	13
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	13
α-helix	246-248	3
β-strand	249-250	2	14
β-strand	253-254	2	14
α-helix	255	1
α-helix	257	1
β-strand	258-259	2	16
β-strand	260-266	7	9
β-strand	267	1	10
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	9
β-strand	304	1	11
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	16
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-367	11
α-helix	372-385	14
α-helix	387-475	89

Chain C: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	17
α-helix	17-31	15
β-strand	35-38	4	17
α-helix	43-50	8
β-strand	59-62	4	17
α-helix	70-73	4
β-strand	76-77	2	17
α-helix	83-86	4
β-strand	89	1	18
α-helix	91-95	5
β-strand	98	1	19
β-strand	103	1	19
β-strand	106-111	6	17
β-strand	114-118	5	20
β-strand	128	1	21
α-helix	132-142	11
β-strand	145-147	3	20
α-helix	154-161	8
β-strand	167-172	6	22
β-strand	175-182	8	22
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	20
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	20
α-helix	246-248	3
β-strand	249	1	21
β-strand	250	1	23
β-strand	253	1	23
β-strand	258-259	2	24
β-strand	260-267	8	17
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	17
β-strand	304	1	18
α-helix	305-311	7
α-helix	315-325	11
β-strand	328-329	2	24
α-helix	336-351	16
α-helix	357-367	11
α-helix	372-385	14
α-helix	389-460	72

Chain D: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	25
α-helix	17-31	15
β-strand	36-38	3	25
α-helix	43-50	8
β-strand	59-62	4	25
α-helix	65-66	2
β-strand	76	1	26
α-helix	83-86	4
β-strand	89	1	27
α-helix	91-95	5
β-strand	98-99	2	28
β-strand	102-103	2	28
β-strand	106-111	6	25
β-strand	114-118	5	29
β-strand	128	1	30
α-helix	129-131	3
α-helix	132-140	9
β-strand	145-147	3	29
α-helix	154-161	8
β-strand	167-172	6	31
β-strand	175-182	8	31
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	29
α-helix	229-231	3
α-helix	232-238	7
β-strand	242-245	4	29
α-helix	246-248	3
β-strand	249	1	30
β-strand	250	1	32
β-strand	253	1	32
β-strand	258-259	2	33
β-strand	260-266	7	25
β-strand	267	1	26
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	25
β-strand	304	1	27
α-helix	305-311	7
α-helix	315-325	11
β-strand	328-329	2	33
α-helix	336-351	16
α-helix	357-368	12
α-helix	372-385	14
α-helix	387-446	60
α-helix	454-475	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion	A, B, C, D	protein	490	Escherichia coli, Saccharomyces cerevisiae	P0AEX9 (AlphaFold model), Q12495 (AlphaFold model)

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

>8DEI_1 Maltodextrin-binding protein,Chromatin assembly factor 1 subunit p90 fusion (chains A, B, C, D)
MRSHHHHHHGKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQV
AATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAV
EALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK
YENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPW
AWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGL
EAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINA
ASGRQTVDEALKDAQTNSGSDITSLYKKAGFLEVLFQGPLKKEEAKREKELKKQQRAEEK
HRKELLRQEEKKKKELKVEEERQRRAELKKQKEEEKRRKEEARLEAKRRKEEERLKKEEE
IRLKEEAKER

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function. Rosas, R., Aguilar, R.R., Arslanovic, N. et al. Elife (2023) 12. DOI 10.7554/eLife.83538 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

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