7ZWA: Ku heterodimer

CryoEM structure of Ku heterodimer bound to DNA and PAXX. Determined by electron microscopy at 2.8 Å resolution. Released 31 May 2023.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Homo sapiens
Chains
5
Atoms
9,038
Mol. weight
184.02 kDa
Ligands
PO4
Released
31 May 2023

Explore 7ZWA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZWA contains 50 α-helices and 54 β-strands across 3 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: 21 helices, 27 β-strands

ElementResiduesLengthSheet
β-strand35-4391
α-helix46-494
α-helix59-7719
β-strand82-8871
β-strand102-10431
β-strand10911
β-strand11212
α-helix113-1208
α-helix127-1348
α-helix143-15614
β-strand161-170101
α-helix174-1774
α-helix180-19617
β-strand198-20471
α-helix239-2435
α-helix251-2533
β-strand257-26263
β-strand268-27473
β-strand27714
α-helix282-2854
β-strand286-28945
β-strand29515
β-strand296-30496
β-strand31016
α-helix313-3153
β-strand316-32277
β-strand325-32957
α-helix331-3366
β-strand344-35293
α-helix353-3553
β-strand366-37053
β-strand375-37628
α-helix378-39215
β-strand394-40183
β-strand409-41683
β-strand419-42029
β-strand426-42839
β-strand431-43663
α-helix440-4423
β-strand443110
α-helix452-4554
α-helix456-46813
β-strand470111
β-strand471112
α-helix481-49515
α-helix500-5045
α-helix511-5188
α-helix521-5299
Chain B: 28 helices, 26 β-strands
ElementResiduesLengthSheet
β-strand8-15813
α-helix18-214
α-helix30-4718
β-strand53-59713
β-strand65113
β-strand77-84813
α-helix88-925
α-helix93-975
α-helix107-12216
β-strand129-135713
α-helix147-15711
β-strand159113
β-strand162-165413
α-helix199-21618
α-helix219-2235
β-strand224-226313
α-helix227-2304
α-helix235-2373
α-helix241-2466
β-strand247-253711
β-strand257-2681211
β-strand277-28047
β-strand289-29796
β-strand30416
α-helix307-3093
β-strand310-31675
β-strand31712
β-strand319-32245
α-helix325-3317
β-strand339-347911
α-helix348-3503
α-helix353-3553
β-strand357-3661011
α-helix3671
α-helix371-38717
β-strand389-396811
α-helix402-4032
β-strand404-412911
β-strand417-424811
β-strand43014
α-helix448-46013
β-strand46213
β-strand464-466314
β-strand473-475314
α-helix479-4813
α-helix483-4842
α-helix485-49915
α-helix504-5096
α-helix510-5167
α-helix518-5192
α-helix520-5256
α-helix527-53610
β-strand540-54128
α-helix542-5432
Chain C: 1 helix, 1 β-strand
ElementResiduesLengthSheet
α-helix191-1955
β-strand201112

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
X-ray repair cross-complementing protein 6Aprotein609Homo sapiensP12956 (AlphaFold model)
X-ray repair cross-complementing protein 5Bprotein732Homo sapiensP13010 (AlphaFold model)
Protein PAXXCprotein204Homo sapiensQ9BUH6 (AlphaFold model)
DNA (5'-d(p*gp*ap*tp*cp*cp*cp*tp*cp*tp*ap*gp*ap*tp*ap*t)-3')DDNA15Homo sapiens
DNA (5'-d(p*cp*gp*ap*tp*ap*tp*cp*tp*ap*gp*ap*gp*gp*gp*ap*tp*c)-3')EDNA16Homo sapiens
Sequence of entity 1 (A), FASTA
>7ZWA_1 X-ray repair cross-complementing protein 6 (chains A)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD
Sequence of entity 2 (B), FASTA
>7ZWA_2 X-ray repair cross-complementing protein 5 (chains B)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI
Sequence of entity 3 (C), FASTA
>7ZWA_3 Protein PAXX (chains C)
MDPLSPPLCTLPPGPEPPRFVCYCEGEESGEGDRGGFNLYVTDAAELWSTCFTPDSLAAL
KARFGLSAAEDITPRFRAACEQQAVALTLQEDRASLTLSGGPSALAFDLSKVPGPEAAPR
LRALTLGLAKRVWSLERRLAAAEETAVSPRKSPRPAGPQLFLPDPDPQRGGPGPGVRRRC
PGESLINPGFKSKKPAGGVDFDET
Sequence of entity 4 (D), FASTA
>7ZWA_4 DNA (5'-D(P*GP*AP*TP*CP*CP*CP*TP*CP*TP*AP*GP*AP*TP*AP*T)-3') (chains D)
GATCCCTCTAGATAT
Sequence of entity 5 (E), FASTA
>7ZWA_5 DNA (5'-D(P*CP*GP*AP*TP*AP*TP*CP*TP*AP*GP*AP*GP*GP*GP*AP*TP*C)-3') (chains E)
GATATCTAGAGGGATC

Ligands and cofactors

IDNameFormulaCopies
PO4Phosphate ionO4 P1

Primary citation

PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Seif-El-Dahan, M., Kefala-Stavridi, A., Frit, P. et al. Sci Adv (2023) 9:eadg2834-eadg2834. DOI 10.1126/sciadv.adg2834 · PubMed

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

Browse structure collections

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