3E0J: DNA polymerase subunit delta-2

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Dec 2008.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,153
Mol. weight: 273.83 kDa
Released: 16 Dec 2008

Explore 3E0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E0J contains 79 α-helices and 113 β-strands across 8 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, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	24-25	2	1
α-helix	26-27	2
β-strand	32-34	3	2
α-helix	37-39	3
α-helix	55-72	18
β-strand	79	1	3
β-strand	91-100	10	3
β-strand	132-136	5	3
β-strand	141-146	6	3
β-strand	158-165	8	3
β-strand	171-178	8	3
β-strand	180	1	4
α-helix	185-189	5
β-strand	195-199	5	5
β-strand	204	1	6
α-helix	209-223	15
α-helix	229-235	7
β-strand	238-244	7	5
β-strand	248	1	6
α-helix	265-287	23
β-strand	292-295	4	5
α-helix	317-320	4
β-strand	325-327	3	5
β-strand	332-336	5	2
β-strand	339-343	5	2
α-helix	347-355	9
α-helix	361-370	10
β-strand	371	1	4
β-strand	401-407	7	2
β-strand	411-416	6	2
β-strand	422-429	8	2
α-helix	431-434	4
β-strand	436-441	6	5
β-strand	446	1	5
β-strand	449-454	6	5

Chain B: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	12-16	5
β-strand	21-22	2	5
α-helix	23-30	8
α-helix	34-52	19
β-strand	58-70	13	5
β-strand	72-81	10	5
α-helix	85-91	7
β-strand	94-104	11	5
α-helix	113-125	13
α-helix	129-131	3
β-strand	135-136	2	1

Chain C: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	24-25	2	7
α-helix	26-27	2
β-strand	32-34	3	8
α-helix	37-39	3
α-helix	55-72	18
β-strand	79	1	9
β-strand	91-100	10	9
β-strand	132-136	5	9
β-strand	141-146	6	9
β-strand	158-165	8	9
β-strand	171-177	7	9
β-strand	180	1	10
α-helix	185-189	5
β-strand	195-199	5	11
β-strand	204	1	12
α-helix	209-223	15
α-helix	229-235	7
β-strand	238-244	7	11
β-strand	248	1	12
α-helix	265-287	23
β-strand	292-295	4	11
α-helix	317-320	4
β-strand	325-327	3	11
β-strand	332-336	5	8
β-strand	339-343	5	8
α-helix	347-355	9
α-helix	361-370	10
β-strand	371	1	10
β-strand	401-407	7	8
β-strand	411-416	6	8
β-strand	422-429	8	8
α-helix	431-434	4
β-strand	436-441	6	11
β-strand	446-454	9	11

Chain D: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	12-16	5
β-strand	21-22	2	11
α-helix	23-30	8
α-helix	34-52	19
β-strand	58-68	11	11
β-strand	73-81	9	11
α-helix	85-91	7
β-strand	95-104	10	11
α-helix	107-108	2
α-helix	113-125	13
α-helix	126-131	6
β-strand	135-136	2	7

Chain E: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	24-25	2	7
α-helix	26-27	2
β-strand	32-34	3	13
α-helix	37-39	3
α-helix	55-73	19
β-strand	79	1	14
β-strand	91-100	10	14
β-strand	132-136	5	14
β-strand	141-146	6	14
β-strand	158-165	8	14
β-strand	171-177	7	14
β-strand	180	1	15
α-helix	185-189	5
β-strand	195-199	5	16
β-strand	204	1	17
α-helix	209-223	15
α-helix	229-235	7
β-strand	238-244	7	16
β-strand	248	1	17
α-helix	265-289	25
β-strand	292-295	4	16
α-helix	317-320	4
β-strand	325-327	3	16
β-strand	332-336	5	13
β-strand	339-343	5	13
α-helix	347-355	9
α-helix	361-370	10
β-strand	371	1	15
β-strand	401-407	7	13
β-strand	411-416	6	13
β-strand	422-429	8	13
α-helix	431-434	4
β-strand	436-441	6	16
β-strand	446-454	9	16

Chain F: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	12-16	5
β-strand	21-22	2	16
α-helix	23-30	8
α-helix	34-52	19
β-strand	58-68	11	16
β-strand	73-81	9	16
α-helix	85-91	7
β-strand	95-104	10	16
α-helix	113-125	13
α-helix	129-131	3
β-strand	135-136	2	7

Chain G: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	24-25	2	18
α-helix	26-27	2
β-strand	32-34	3	19
α-helix	37-39	3
α-helix	55-73	19
β-strand	79	1	20
β-strand	91-100	10	20
β-strand	132-136	5	20
β-strand	141-146	6	20
β-strand	158-165	8	20
β-strand	171-177	7	20
β-strand	180	1	21
α-helix	185-189	5
β-strand	195-199	5	22
β-strand	204	1	23
α-helix	209-223	15
α-helix	229-235	7
β-strand	238-244	7	22
β-strand	248	1	23
α-helix	265-289	25
β-strand	292-295	4	22
α-helix	313-315	3
α-helix	317-320	4
β-strand	325-327	3	22
β-strand	332-336	5	19
β-strand	339-343	5	19
α-helix	347-355	9
α-helix	361-370	10
β-strand	371	1	21
β-strand	401-407	7	19
β-strand	411-416	6	19
β-strand	422-429	8	19
α-helix	431-434	4
β-strand	436-441	6	22
β-strand	446-454	9	22

Chain H: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	12-16	5
β-strand	21-22	2	22
α-helix	23-26	4
α-helix	27-31	5
α-helix	34-52	19
β-strand	58-68	11	22
β-strand	73-81	9	22
α-helix	85-91	7
β-strand	95-104	10	22
α-helix	113-125	13
α-helix	129-131	3
β-strand	135-136	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase subunit delta-2	A, C, E, G	protein	476	Homo sapiens	P49005 (AlphaFold model)
DNA polymerase subunit delta-3	B, D, F, H	protein	144	Homo sapiens	Q15054 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3E0J_1 DNA polymerase subunit delta-2 (chains A, C, E, G)
HHHHHHGMFSEQAAQRAHTLLSPPSANNATFARVPVATYTNSSQPFRLGERSFSRQYAHI
YATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSE
EHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLV
EDYCFADLAPQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQC
SAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVD
VMPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIF
RYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSK
IIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISFSGFGAEDDDLGGLGLGP

Sequence of entity 2 (B, D, F, H), FASTA

>3E0J_2 DNA polymerase subunit delta-3 (chains B, D, F, H)
MADQLYLENIDEFVTDQNKIVTYKWLSYTLGVHVNQAKQMLYDYVERKRKENSGAQLHVT
YLVSGSLIQNGHSCHKVAVVREDKLEAVKSKLAVTASIHVYSIQKAMLKDSGPLFNTDYD
ILKSNLQNCSKFSAIQCAAAVPRA

Primary citation

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta. Baranovskiy, A.G., Babayeva, N.D., Liston, V.G. et al. Cell Cycle (2008) 7:3026-3036. PubMed

Other PDB entries of the same protein (UniProt P49005 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TNY 3.08 Å, Processive human polymerase delta holoenzyme
9EKB 3.65 Å, Cryo-EM structure of apo-form human DNA polymerase delta
6TNZ 4.05 Å, Human polymerase delta-FEN1-PCNA toolbelt
6S1M 4.27 Å, Human polymerase delta holoenzyme Conformer 1
6S1N 4.86 Å, Human polymerase delta holoenzyme Conformer 2
6S1O 8.1 Å, Human polymerase delta holoenzyme Conformer 3

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