4E2I: Large T antigen

The Complex Structure of the SV40 Helicase Large T Antigen and p68 Subunit of DNA Polymerase Alpha-Primase. Determined by X-ray diffraction at 5.0 Å resolution. Released 13 Jun 2012.

Method: X-ray diffraction
Resolution: 5.0 Å
Organisms: Simian virus 40, Homo sapiens
Chains: 23
Atoms: 41,874
Mol. weight: 598.25 kDa
Ligands: ZN
Released: 13 Jun 2012

Explore 4E2I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4E2I contains 316 α-helices and 132 β-strands across 23 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.

Chains 1, 2, 4, 6, 8, U and W: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	5-14	10
α-helix	21-28	8
α-helix	30-33	4
α-helix	38-45	8
α-helix	48-51	4
α-helix	64-66	3
α-helix	71-73	3

Chains 3, 5, 7 and 9: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	5-14	10
α-helix	21-33	13
α-helix	38-45	8
α-helix	48-51	4
α-helix	64-66	3
α-helix	71-73	3

Chains A and D: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	267-269	3
α-helix	270-280	11
α-helix	285-292	8
α-helix	303-306	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	416	1	1
β-strand	419	1	1
β-strand	421-425	5	2
α-helix	432-443	12
β-strand	445-446	2	2
α-helix	457-461	5
β-strand	469-472	4	2
α-helix	490-495	6
α-helix	498-502	5
β-strand	506	1	3
β-strand	509	1	4
β-strand	517	1	4
β-strand	520	1	3
α-helix	521-522	2
β-strand	524-528	5	2
α-helix	535-538	4
β-strand	541-544	4	2
α-helix	551-557	7
α-helix	561-565	5
α-helix	572-581	10
α-helix	585-587	3
α-helix	593-606	14
α-helix	609-621	13

Chains B, C, F, G, H, I, J and K: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-292	8
α-helix	303-306	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	416	1	5
β-strand	419	1	5
β-strand	421-425	5	6
α-helix	432-443	12
β-strand	445-446	2	6
α-helix	457-461	5
β-strand	469-472	4	6
α-helix	490-495	6
α-helix	498-502	5
β-strand	506	1	7
β-strand	509	1	8
β-strand	517	1	8
β-strand	520	1	7
α-helix	521-522	2
β-strand	524-528	5	6
α-helix	535-538	4
β-strand	541-544	4	6
α-helix	551-557	7
α-helix	561-565	5
α-helix	572-581	10
α-helix	585-587	3
α-helix	593-606	14
α-helix	609-621	13

Chain E: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-292	8
α-helix	303-306	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	416	1	17
β-strand	419	1	17
β-strand	421-425	5	18
α-helix	432-443	12
β-strand	445-446	2	18
α-helix	457-461	5
β-strand	469-472	4	18
α-helix	490-495	6
α-helix	498-502	5
β-strand	506	1	19
β-strand	509-510	2	20
β-strand	515-517	3	20
β-strand	520	1	19
α-helix	521-522	2
β-strand	524-528	5	18
α-helix	535-538	4
β-strand	541-544	4	18
α-helix	551-557	7
α-helix	561-565	5
α-helix	572-581	10
α-helix	585-587	3
α-helix	593-606	14
α-helix	609-621	13

Chain L: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	267-269	3
α-helix	270-280	11
α-helix	285-292	8
α-helix	303-306	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	416	1	45
β-strand	419	1	45
β-strand	421-425	5	46
α-helix	432-443	12
β-strand	445-446	2	46
α-helix	457-461	5
β-strand	469-472	4	46
α-helix	490-495	6
α-helix	498-502	5
β-strand	506	1	47
β-strand	509-510	2	48
β-strand	515-517	3	48
β-strand	520	1	47
α-helix	521-522	2
β-strand	524-528	5	46
α-helix	535-538	4
β-strand	541-544	4	46
α-helix	551-557	7
α-helix	561-565	5
α-helix	572-581	10
α-helix	585-587	3
α-helix	593-606	14
α-helix	609-621	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large T antigen	A, B, C, D, E, F, G, H, I, J, K, L	protein	362	Simian virus 40	P03070 (AlphaFold model)
DNA polymerase alpha subunit B	1, 2, 3, 4, 5, 6, 7, 8, 9, U, W	protein	78	Homo sapiens	Q14181 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>4E2I_1 Large T antigen (chains A, B, C, D, E, F, G, H, I, J, K, L)
KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAA
IFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIE
EWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGG
KALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSV
KVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLE
KRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGV
LD

Sequence of entity 2 (1, 2, 3, 4, 5, 6, 7, 8, 9, U, W), FASTA

>4E2I_2 DNA polymerase alpha subunit B (chains 1, 2, 3, 4, 5, 6, 7, 8, 9, U, W)
MSASAQQLAEELQIFGLDCEEALIEKLVELCVQYGQNEEGMVGELIAFCTSTHKVGLTSE
ILNSFEHEFLSKRLSKAR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Structural basis for the interaction of a hexameric replicative helicase with the regulatory subunit of human DNA polymerase alpha-primase. Zhou, B., Arnett, D.R., Yu, X. et al. J Biol Chem (2012) 287:26854-26866. DOI 10.1074/jbc.M112.363655 · PubMed

Other PDB entries of the same protein (UniProt P03070 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FUF 1.45 Å, Crystal structure of the SV40 large T antigen origin-binding domain
2IPR 1.5 Å, Origin binding domain of the SV40 large T antigen (residues 131-259). P21 crystal form
3QK2 1.64 Å, Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin…
2ITL 1.65 Å, The origin binding domain of the SV40 large T antigen bound to the functional pen…
3QN2 1.66 Å, Structure-based design of a disulfide-linked oligomeric form of the Simian Virus 40…
5D9I 1.7 Å, SV40 Large T antigen origin binding domain bound to artificial DNA fork
4RXH 1.76 Å, Crystal Structure of Importin-alpha from Neurospora crassa complexed with SV40NLS
1SVM 1.94 Å, Co-crystal structure of SV40 large T antigen helicase domain and ATP
1SVL 1.95 Å, Co-crystal structure of SV40 large T antigen helicase domain and ADP
1Q1S 2.3 Å, Mouse Importin alpha- phosphorylated SV40 CN peptide complex
2NL8 2.3 Å, The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp…
2NTC 2.4 Å, Crystal Structure of sv40 large T antigen origin binding domain with DNA

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