6ERG: Complex of XLF and heterodimer Ku

Complex of XLF and heterodimer Ku bound to DNA. Determined by X-ray diffraction at 2.9 Å resolution. Released 17 Oct 2018.

Method

X-ray diffraction

Resolution

2.9 Å

Organisms

Homo sapiens, Synthetic construct

Chains

10

Atoms

18,989

Mol. weight

293 kDa

Released

17 Oct 2018

Explore 6ERG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ERG contains 106 α-helices and 106 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.

Chains A and D: 26 helices, 27 β-strands

Molecules and chains

>6ERG_1 X-ray repair cross-complementing protein 6 (chains A, D)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRK

>6ERG_2 X-ray repair cross-complementing protein 5 (chains B, E)
MHHHHHHHHHHENLYFQGVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQ
RQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQ
QADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQF
FLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDE
IYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKT
LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL
GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANP
QVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSL
AKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVT
TKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQ

>6ERG_3 Non-homologous end-joining factor 1 (chains C, F)
SKVKRKKPRGLFS

>6ERG_4 DNA (21-MER) (chains H, K)
GTTTTTAGTTTATTGGGCGCG

>6ERG_5 DNA (34-MER) (chains M, R)
CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAAC

Primary citation

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nemoz, C., Ropars, V., Frit, P. et al. Nat Struct Mol Biol (2018) 25:971-980. DOI 10.1038/s41594-018-0133-6 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P12956 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 8AG4 2.46 Å, Vaccinia C16 protein bound to Ku70/Ku80
• 1JEY 2.5 Å, Crystal Structure of the Ku heterodimer bound to DNA
• 3RZX 2.61 Å, Mouse importin alpha-Ku70 NLS peptide complex
• 7ZYG 2.68 Å, CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF
• 1JEQ 2.7 Å, Crystal Structure of the Ku Heterodimer
• 7ZVT 2.74 Å, CryoEM structure of Ku heterodimer bound to DNA
• 6ERH 2.8 Å, Complex of XLF and heterodimer Ku bound to DNA
• 7ZWA 2.8 Å, CryoEM structure of Ku heterodimer bound to DNA and PAXX
• 9CQ3 2.8 Å, The gap-filling complex with Pol mu engaged in the NHEJ pathway
• 9GYF 2.8 Å, Ku70/80 with PAXX peptide mutation K193R
• 9N81 2.8 Å, A gap-filling complex with Pol mu engaged in the NHEJ Pathway
• 7Z87 2.91 Å, DNA-PK in the active state

Browse structure collections

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