8ASC: Ku70/80 binds to the Ku-binding motif of PAXX

Ku70/80 binds to the Ku-binding motif of PAXX. Determined by X-ray diffraction at 2.95 Å resolution. Released 21 Jun 2023.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Homo sapiens, DNA molecule
Chains: 18
Atoms: 36,383
Mol. weight: 573.91 kDa
Released: 21 Jun 2023

Explore 8ASC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ASC contains 206 α-helices and 205 β-strands across 9 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	46-49	4
α-helix	57-58	2
α-helix	59-76	18
β-strand	82-88	7	1
β-strand	94	1	1
β-strand	102-109	8	1
α-helix	113-120	8
α-helix	124-134	11
α-helix	143-155	13
β-strand	161-170	10	1
α-helix	180-196	17
β-strand	198-204	7	1
β-strand	205	1	2
α-helix	233-235	3
β-strand	236	1	2
α-helix	239-248	10
β-strand	257-262	6	3
β-strand	268-274	7	3
β-strand	277	1	4
α-helix	282-285	4
β-strand	286-289	4	5
β-strand	296-304	9	6
β-strand	310	1	6
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	7
β-strand	325-329	5	7
α-helix	331-336	6
β-strand	344	1	8
β-strand	345-352	8	3
α-helix	353-355	3
β-strand	366-370	5	3
β-strand	375-376	2	9
α-helix	378-392	15
β-strand	394-400	7	3
β-strand	401	1	8
β-strand	409-416	8	3
α-helix	417-418	2
β-strand	419-420	2	10
β-strand	426-428	3	10
β-strand	431-436	6	3
β-strand	443	1	11
α-helix	444-445	2
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	11
α-helix	481-494	14
α-helix	498-500	3
α-helix	511-517	7
α-helix	520-529	10

Chain B: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	12
α-helix	18-21	4
α-helix	28-29	2
α-helix	30-47	18
β-strand	53-59	7	12
β-strand	65	1	12
α-helix	70-72	3
β-strand	77-84	8	12
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	129-135	7	12
α-helix	147-157	11
β-strand	159-165	7	12
α-helix	170-174	5
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	12
α-helix	227-231	5
α-helix	238-240	3
α-helix	241-245	5
β-strand	247-252	6	11
β-strand	259-268	10	11
β-strand	277-280	4	7
β-strand	289-297	9	6
α-helix	303	1
β-strand	304	1	6
α-helix	305-306	2
β-strand	310-316	7	5
β-strand	319-322	4	5
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	417-424	8	11
β-strand	430	1	4
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	3
β-strand	464-465	2	13
α-helix	473	1
β-strand	474-475	2	13
α-helix	479-481	3
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	518-519	2
α-helix	520-536	17
β-strand	540-541	2	9

Chain E: 20 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	14
α-helix	46-49	4
α-helix	59-77	19
β-strand	82-88	7	14
β-strand	94	1	14
β-strand	102-109	8	14
α-helix	113-120	8
α-helix	124-134	11
α-helix	143-155	13
β-strand	161-170	10	14
α-helix	175-177	3
α-helix	180-196	17
β-strand	198-204	7	14
α-helix	235-236	2
α-helix	238-243	6
β-strand	257-262	6	15
β-strand	268-274	7	15
β-strand	277	1	16
α-helix	282-285	4
β-strand	286-289	4	17
β-strand	296-304	9	18
β-strand	310	1	18
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	19
β-strand	325-329	5	19
α-helix	331-338	8
β-strand	341	1	20
β-strand	344-352	9	15
α-helix	353-355	3
β-strand	366-370	5	15
β-strand	375-376	2	21
α-helix	378-392	15
β-strand	394-401	8	15
β-strand	406	1	20
β-strand	409-416	8	15
β-strand	419-420	2	22
β-strand	426-428	3	22
β-strand	431-436	6	15
β-strand	443	1	23
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	23
α-helix	481-494	14
α-helix	511-517	7
α-helix	520-529	10

Chain F: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	24
α-helix	18-21	4
α-helix	28-29	2
α-helix	30-47	18
β-strand	54-59	6	24
β-strand	65	1	24
β-strand	77-84	8	24
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	129-135	7	24
α-helix	147-157	11
β-strand	159-165	7	24
α-helix	168-171	4
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	24
α-helix	227-231	5
α-helix	238-240	3
α-helix	241-245	5
β-strand	246-253	8	23
β-strand	257-268	12	23
β-strand	277-280	4	19
β-strand	289-297	9	18
α-helix	303	1
β-strand	304	1	18
α-helix	305-306	2
β-strand	310-316	7	17
β-strand	319-322	4	17
α-helix	325-331	7
β-strand	341-347	7	23
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	23
α-helix	367	1
α-helix	371-387	17
β-strand	389-395	7	23
α-helix	402-403	2
β-strand	404-412	9	23
β-strand	417-423	7	23
β-strand	430	1	16
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	15
β-strand	464-466	3	25
α-helix	472	1
β-strand	473-475	3	25
α-helix	479-481	3
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	518-519	2
α-helix	520-536	17
β-strand	540-541	2	21

Chain K: 22 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	26
α-helix	46-49	4
α-helix	57-58	2
α-helix	59-76	18
β-strand	81-88	8	26
β-strand	94	1	26
β-strand	102-109	8	26
α-helix	113-120	8
α-helix	124-134	11
α-helix	143-155	13
β-strand	161-170	10	26
α-helix	180-196	17
β-strand	198-204	7	26
β-strand	205	1	27
α-helix	234-235	2
β-strand	236	1	27
α-helix	239-248	10
β-strand	257-262	6	28
β-strand	268-274	7	28
β-strand	277	1	29
α-helix	282-285	4
β-strand	286-287	2	30
β-strand	297-304	8	31
β-strand	310	1	31
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	32
β-strand	325-329	5	32
α-helix	331-336	6
β-strand	341	1	33
β-strand	344-352	9	28
α-helix	353-355	3
β-strand	366-370	5	28
β-strand	375-376	2	34
α-helix	378-392	15
β-strand	394-401	8	28
β-strand	406	1	33
β-strand	409-416	8	28
α-helix	417-418	2
β-strand	419-420	2	35
β-strand	426-428	3	35
β-strand	431-436	6	28
β-strand	443	1	36
α-helix	444-445	2
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	36
α-helix	481-494	14
α-helix	511-517	7
α-helix	520-529	10

Chain L: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	37
α-helix	18-21	4
α-helix	28-29	2
α-helix	30-47	18
β-strand	53-59	7	37
β-strand	65	1	37
α-helix	70-72	3
β-strand	77-84	8	37
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	129-135	7	37
α-helix	147-157	11
β-strand	159-165	7	37
α-helix	194-196	3
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	37
α-helix	227-231	5
α-helix	238-240	3
α-helix	241-245	5
β-strand	247-253	7	36
β-strand	257-268	12	36
β-strand	277-280	4	32
β-strand	289-296	8	31
α-helix	303	1
β-strand	304	1	31
α-helix	305-306	2
β-strand	312-316	5	30
β-strand	319-322	4	30
α-helix	325-331	7
β-strand	339-347	9	36
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	36
α-helix	367	1
α-helix	371-387	17
β-strand	389-396	8	36
α-helix	402-403	2
β-strand	404-412	9	36
β-strand	417-424	8	36
β-strand	430	1	29
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	28
β-strand	464-465	2	38
β-strand	474-475	2	38
α-helix	479-481	3
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	518-519	2
α-helix	520-536	17
β-strand	540-541	2	34

Chain O: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	35-43	9	39
α-helix	46-49	4
α-helix	59-77	19
β-strand	82-88	7	39
β-strand	94	1	39
β-strand	102-109	8	39
α-helix	113-120	8
α-helix	124-134	11
α-helix	143-155	13
β-strand	161-170	10	39
α-helix	175-177	3
α-helix	180-196	17
β-strand	198-204	7	39
α-helix	235-236	2
α-helix	238-243	6
β-strand	257-262	6	40
β-strand	268-274	7	40
β-strand	277	1	41
α-helix	282-285	4
β-strand	286-289	4	42
β-strand	296-304	9	43
β-strand	310	1	43
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	44
β-strand	325-329	5	44
α-helix	331-336	6
α-helix	342	1
β-strand	344	1	45
β-strand	345-352	8	40
α-helix	353-355	3
β-strand	366-370	5	40
β-strand	375-376	2	46
α-helix	378-392	15
β-strand	394-400	7	40
β-strand	401	1	45
β-strand	409-416	8	40
α-helix	417-418	2
β-strand	419-420	2	47
β-strand	426-428	3	47
β-strand	431-436	6	40
β-strand	443	1	48
α-helix	444-445	2
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	48
β-strand	471	1	49
α-helix	481-494	14
α-helix	511-529	19

Chain P: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	50
α-helix	18-21	4
α-helix	28-29	2
α-helix	30-47	18
β-strand	53-59	7	50
β-strand	77-84	8	50
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	129-135	7	50
α-helix	147-157	11
β-strand	159-165	7	50
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	50
α-helix	227-231	5
α-helix	241-245	5
β-strand	247-253	7	48
β-strand	257-268	12	48
β-strand	277-280	4	44
β-strand	289-297	9	43
α-helix	303	1
β-strand	304	1	43
α-helix	305-306	2
β-strand	310-316	7	42
β-strand	319-322	4	42
α-helix	325-331	7
β-strand	341-347	7	48
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	48
α-helix	367	1
α-helix	371-387	17
β-strand	389-395	7	48
α-helix	402-403	2
β-strand	404-412	9	48
β-strand	417-423	7	48
β-strand	430	1	41
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	40
β-strand	464-466	3	51
α-helix	472	1
β-strand	473-475	3	51
α-helix	479-481	3
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-516	7
α-helix	518-519	2
α-helix	520-536	17
β-strand	540-541	2	46

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
X-ray repair cross-complementing protein 6	A, E, K, O	protein	544	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B, F, L, P	protein	572	Homo sapiens	P13010 (AlphaFold model)
DNA (5'-d(pcpgpgpaptpcpgpapgpgpgpcpcpcpgpaptpap*t)-3')	C, G, M, Q	DNA	30	DNA molecule
DNA (5'-d(pgpgpgpcpcpcptpcpgpaptpcpcpg)-3')	D, H, N, R	DNA	15	DNA molecule
Protein PAXX	J, T	protein	28	Homo sapiens	Q9BUH6 (AlphaFold model)

Sequence of entity 1 (A, E, K, O), FASTA

>8ASC_1 X-ray repair cross-complementing protein 6 (chains A, E, K, O)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRK

Sequence of entity 2 (B, F, L, P), FASTA

>8ASC_2 X-ray repair cross-complementing protein 5 (chains B, F, L, P)
MHHHHHHHHHHENLYFQGVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQ
RQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQ
QADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQF
FLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDE
IYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKT
LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL
GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANP
QVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSL
AKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVT
TKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQ

Sequence of entity 3 (C, G, M, Q), FASTA

>8ASC_3 DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3') (chains C, G, M, Q)
CGGATCGAGGGCCCGATATCTAGAGGGATC

Sequence of entity 4 (D, H, N, R), FASTA

>8ASC_4 DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3') (chains D, H, N, R)
CGGGCCCTCGATCCG

Sequence of entity 5 (J, T), FASTA

>8ASC_5 Protein PAXX (chains J, T)
RRRCPGESLINPGFKSKKPAGGVDFDET

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
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
6ERG 2.9 Å, Complex of XLF and heterodimer Ku bound to DNA

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