7ZVT: Ku heterodimer

CryoEM structure of Ku heterodimer bound to DNA. Determined by electron microscopy at 2.74 Å resolution. Released 24 May 2023.

Method
Electron microscopy
Resolution
2.74 Å
Organism
Homo sapiens
Chains
4
Atoms
8,842
Mol. weight
162.57 kDa
Ligands
IHP
Released
24 May 2023

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

Secondary structure: helices and β-sheets

7ZVT contains 50 α-helices and 51 β-strands across 2 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: 20 helices, 27 β-strands

ElementResiduesLengthSheet
β-strand35-4391
α-helix46-494
α-helix59-7618
β-strand82-8871
β-strand9411
β-strand102-10981
α-helix113-1208
α-helix124-13512
α-helix143-15614
β-strand161-170101
α-helix180-19617
β-strand199-20461
β-strand20512
α-helix213-2164
β-strand23612
α-helix239-25012
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-strand316-31947
β-strand328-32927
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-helix437-4382
β-strand443110
α-helix452-4554
α-helix456-46813
β-strand470110
α-helix481-49414
α-helix500-5045
α-helix511-5188
α-helix521-5299
Chain B: 30 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand8-15811
α-helix18-214
α-helix30-4718
β-strand53-59711
β-strand65111
β-strand77-84811
α-helix88-925
α-helix93-975
α-helix107-12115
β-strand129-135711
α-helix147-15610
β-strand159-165711
α-helix194-1963
α-helix199-21517
α-helix219-2224
β-strand224-226311
α-helix227-2315
α-helix241-2466
β-strand247-252610
β-strand258-2681110
α-helix2761
β-strand277-28047
β-strand289-29796
β-strand304-30526
α-helix307-3093
β-strand310-31675
β-strand319-32245
α-helix325-3306
β-strand339-347910
α-helix348-3503
α-helix353-3553
β-strand357-3661010
α-helix3671
α-helix371-38717
β-strand389-396810
α-helix402-4032
β-strand404-412910
β-strand417-424810
α-helix4251
α-helix427-4293
β-strand43014
α-helix448-46013
β-strand46213
β-strand464-465212
α-helix467-4693
β-strand474-475212
α-helix479-4813
α-helix483-4842
α-helix485-49915
α-helix504-5096
α-helix510-5156
α-helix520-5256
α-helix527-53610
β-strand540-54128

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (5'-d(p*tp*cp*cp*cp*tp*cp*tp*ap*gp*ap*tp*ap*tp*c)-3')CDNA14Homo sapiens
DNA (5'-d(p*cp*gp*ap*tp*ap*tp*cp*tp*ap*gp*ap*gp*gp*gp*ap*t)-3')DDNA16Homo sapiens
X-ray repair cross-complementing protein 6Aprotein609Homo sapiensP12956 (AlphaFold model)
X-ray repair cross-complementing protein 5Bprotein732Homo sapiensP13010 (AlphaFold model)
Sequence of entity 1 (C), FASTA
>7ZVT_1 DNA (5'-D(P*TP*CP*CP*CP*TP*CP*TP*AP*GP*AP*TP*AP*TP*C)-3') (chains C)
TCCCTCTAGATATC
Sequence of entity 2 (D), FASTA
>7ZVT_2 DNA (5'-D(P*CP*GP*AP*TP*AP*TP*CP*TP*AP*GP*AP*GP*GP*GP*AP*T)-3') (chains D)
CGATATCTAGAGGGAT
Sequence of entity 3 (A), FASTA
>7ZVT_3 X-ray repair cross-complementing protein 6 (chains A)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL
EALTKHFQD
Sequence of entity 4 (B), FASTA
>7ZVT_4 X-ray repair cross-complementing protein 5 (chains B)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P61

Primary citation

Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction. Kefala Stavridi, A., Gontier, A., Morin, V. et al. Nucleic Acids Res (2023) 51:11732-11747. DOI 10.1093/nar/gkad863 · 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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