4GDF: A Crystal Structure of SV40 Large T Antigen

A Crystal Structure of SV40 Large T Antigen. Determined by X-ray diffraction at 2.8 Å resolution. Released 10 Apr 2013.

Method

X-ray diffraction

Resolution

2.8 Å

Organism

Simian virus 40

Chains

8

Atoms

18,835

Mol. weight

269.43 kDa

Ligands

ZN

Released

10 Apr 2013

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

Secondary structure: helices and β-sheets

4GDF contains 112 α-helices and 58 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: 28 helices, 16 β-strands

Molecules and chains

>4GDF_1 Large T antigen (chains A, B, E, F)
KVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSY
NHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPG
GLKEHDFNPEEAEETKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQ
PSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLD
RMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDS
GKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQG
INNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPK
DYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLS
VYQKMKFNVAMGIGVLD

>4GDF_2 DNA (32-MER) (chains C, G)
ACTACTTCTGGAATAGCTCAGAGGCCGAGGCG

>4GDF_3 DNA (32-MER) (chains D, H)
CGCCTCGGCCTCTGAGCTATTCCAGAAGTAGT

Ligands and cofactors

Primary citation

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen. Chang, Y.P., Xu, M., Machado, A.C. et al. Cell Rep (2013) 3:1117-1127. DOI 10.1016/j.celrep.2013.03.002 · PubMed

Related structures

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

Browse structure collections

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