7ZYG: Ku heterodimer

CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF. Determined by electron microscopy at 2.68 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,914
Mol. weight: 217.07 kDa
Ligands: PO4
Released: 7 Jun 2023

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

Secondary structure: helices and β-sheets

7ZYG contains 51 α-helices and 54 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: 23 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	1
α-helix	59-77	19
β-strand	82-88	7	1
β-strand	90	1	2
β-strand	94	1	1
β-strand	102-109	8	1
β-strand	112	1	3
α-helix	113-119	7
α-helix	120-122	3
α-helix	128-134	7
β-strand	137	1	2
α-helix	143-155	13
β-strand	161-170	10	1
α-helix	175-178	4
α-helix	180-196	17
β-strand	198-204	7	1
α-helix	239-243	5
α-helix	251-253	3
β-strand	257-262	6	4
β-strand	268-274	7	4
β-strand	277	1	5
α-helix	282-285	4
β-strand	286-289	4	6
β-strand	295	1	6
β-strand	297-303	7	7
α-helix	313-315	3
β-strand	316-322	7	8
β-strand	325-329	5	8
α-helix	331-336	6
β-strand	344-352	9	4
α-helix	353-355	3
β-strand	366-370	5	4
β-strand	375-376	2	9
α-helix	378-392	15
β-strand	394-401	8	4
β-strand	409-416	8	4
β-strand	419-420	2	10
β-strand	426-428	3	10
β-strand	431-437	7	4
α-helix	438	1
α-helix	440-442	3
β-strand	443	1	11
α-helix	444-448	5
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	11
β-strand	471	1	12
α-helix	481-494	14
α-helix	500-504	5
α-helix	511-518	8
α-helix	521-529	9

Chain B: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	13
α-helix	18-20	3
α-helix	30-47	18
β-strand	53-59	7	13
β-strand	65	1	13
β-strand	77-84	8	13
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-120	14
β-strand	130-135	6	13
α-helix	147-157	11
β-strand	160-165	6	13
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	13
α-helix	227-233	7
α-helix	237-240	4
α-helix	243-246	4
β-strand	247-252	6	11
β-strand	258-268	11	11
β-strand	277-280	4	8
α-helix	286-288	3
β-strand	290-296	7	7
β-strand	305	1	7
α-helix	307-309	3
β-strand	310-316	7	6
β-strand	317	1	3
β-strand	319-322	4	6
α-helix	325-331	7
β-strand	339-347	9	11
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	11
α-helix	367	1
α-helix	371-387	17
β-strand	389-396	8	11
α-helix	402-403	2
β-strand	404-412	9	11
β-strand	417-423	7	11
β-strand	430	1	5
α-helix	448-460	13
β-strand	462	1	4
β-strand	464-467	4	14
β-strand	472-475	4	14
α-helix	483-484	2
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-515	6
α-helix	520-525	6
α-helix	527-536	10
β-strand	540-541	2	9

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	191-195	5
β-strand	201	1	12

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	296-298	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
X-ray repair cross-complementing protein 6	A	protein	609	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B	protein	732	Homo sapiens	P13010 (AlphaFold model)
Protein PAXX	C	protein	204	Homo sapiens	Q9BUH6 (AlphaFold model)
Non-homologous end-joining factor 1	F	protein	299	Homo sapiens	Q9H9Q4 (AlphaFold model)
DNA	D	DNA	15	Homo sapiens
DNA	E	DNA	15	Homo sapiens

Sequence of entity 1 (A), FASTA

>7ZYG_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

>7ZYG_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

>7ZYG_3 Protein PAXX (chains C)
MDPLSPPLCTLPPGPEPPRFVCYCEGEESGEGDRGGFNLYVTDAAELWSTCFTPDSLAAL
KARFGLSAAEDITPRFRAACEQQAVALTLQEDRASLTLSGGPSALAFDLSKVPGPEAAPR
LRALTLGLAKRVWSLERRLAAAEETAVSPRKSPRPAGPQLFLPDPDPQRGGPGPGVRRRC
PGESLINPGFKSKKPAGGVDFDET

Sequence of entity 4 (F), FASTA

>7ZYG_4 Non-homologous end-joining factor 1 (chains F)
MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKE
LNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWN
FHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLK
TEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGDPHT
SNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGLFS

Sequence of entity 5 (D), FASTA

>7ZYG_5 DNA (chains D)
ATCCCTCTAGATATC

Sequence of entity 6 (E), FASTA

>7ZYG_6 DNA (chains E)
GATATCTAGAGGGAT

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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:

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
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
6ERG 2.9 Å, Complex of XLF and heterodimer Ku bound to DNA
7Z87 2.91 Å, DNA-PK in the active state

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