9GYF: Ku70/80 with PAXX peptide mutation K193R

Ku70/80 with PAXX peptide mutation K193R. Determined by electron microscopy at 2.8 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,717
Mol. weight: 164.75 kDa
Ligands: PO4
Released: 15 Oct 2025

Explore 9GYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GYF contains 53 α-helices and 53 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: 22 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	1
α-helix	46-49	4
α-helix	57-58	2
α-helix	59-77	19
β-strand	82-88	7	1
β-strand	94	1	1
β-strand	102-109	8	1
α-helix	113-120	8
α-helix	127-134	8
α-helix	143-156	14
β-strand	161-169	9	1
α-helix	180-196	17
β-strand	199-202	4	1
α-helix	217-219	3
α-helix	239-243	5
α-helix	251-253	3
β-strand	257	1	2
β-strand	260-262	3	2
β-strand	268-274	7	2
β-strand	277	1	3
α-helix	279-285	7
β-strand	286-289	4	4
β-strand	295	1	4
β-strand	296-304	9	5
β-strand	310	1	5
β-strand	316-321	6	6
β-strand	326-329	4	6
α-helix	331-336	6
β-strand	344-352	9	2
α-helix	353-355	3
β-strand	366-370	5	2
β-strand	375-376	2	7
α-helix	378-392	15
β-strand	394-401	8	2
β-strand	409-416	8	2
β-strand	419-420	2	8
β-strand	426-428	3	8
β-strand	431-437	7	2
α-helix	438	1
α-helix	440-442	3
β-strand	443	1	9
α-helix	456-468	13
β-strand	470	1	9
α-helix	475-477	3
α-helix	481-495	15
α-helix	500-504	5
α-helix	511-518	8
α-helix	521-529	9

Chain B: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	10
α-helix	18-20	3
α-helix	30-47	18
β-strand	53-59	7	10
β-strand	65	1	10
β-strand	77-84	8	10
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-119	13
β-strand	129-135	7	10
α-helix	147-157	11
β-strand	159	1	10
β-strand	162-165	4	10
α-helix	199-215	17
α-helix	218-223	6
β-strand	224-226	3	10
α-helix	227-230	4
α-helix	241-246	6
β-strand	247-253	7	9
β-strand	257-268	12	9
α-helix	275-276	2
β-strand	277-280	4	6
β-strand	289-297	9	5
α-helix	300-302	3
β-strand	304-305	2	5
α-helix	307-309	3
β-strand	310-316	7	4
β-strand	319-322	4	4
α-helix	325-331	7
α-helix	333-335	3
β-strand	339-347	9	9
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	9
α-helix	367	1
α-helix	371-387	17
β-strand	389-396	8	9
α-helix	402-403	2
β-strand	404-412	9	9
β-strand	417-424	8	9
α-helix	425-426	2
α-helix	427-429	3
β-strand	430	1	3
α-helix	448-460	13
β-strand	462	1	2
β-strand	464-466	3	11
β-strand	473-475	3	11
α-helix	479-481	3
α-helix	483-484	2
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	520-525	6
α-helix	528-536	9
β-strand	540-541	2	7

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	183	1	12
β-strand	191	1	12
α-helix	192-195	4

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	23	Homo sapiens	Q9BUH6 (AlphaFold model)
DNA1	D	DNA	15	Homo sapiens
DNA2	E	DNA	16	Homo sapiens

Sequence of entity 1 (A), FASTA

>9GYF_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

>9GYF_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

>9GYF_3 Protein PAXX (chains C)
CPGESLINPGFKSRKPAGGVDFD

Sequence of entity 4 (D), FASTA

>9GYF_4 DNA1 (chains D)
GATCCCTCTAGATAT

Sequence of entity 5 (E), FASTA

>9GYF_5 DNA2 (chains E)
GATATCTAGAGGGATC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Primary citation

Ku70/80 with PAXX peptide mutation K193R. Chaplin, A.K., Malewicz, M. To be published.

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
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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