6ERF: Complex of APLF factor and Ku heterodimer

Complex of APLF factor and Ku heterodimer bound to DNA. Determined by X-ray diffraction at 3.01 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 3.01 Å
Organisms: Homo sapiens, synthetic construct
Chains: 20
Atoms: 35,411
Mol. weight: 588.18 kDa
Released: 17 Oct 2018

Explore 6ERF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ERF contains 197 α-helices and 206 β-strands across 12 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, 25 β-strands

Element	Residues	Length	Sheet
β-strand	37-43	7	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	125-134	10
α-helix	143-153	11
β-strand	164-170	7	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	239-250	12
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
α-helix	313-315	3
β-strand	316-322	7	7
β-strand	325-329	5	7
α-helix	331-336	6
β-strand	344-352	9	3
α-helix	353-355	3
β-strand	366-370	5	3
β-strand	375-376	2	8
α-helix	378-392	15
β-strand	394-401	8	3
β-strand	409-416	8	3
α-helix	417-418	2
β-strand	419-420	2	9
β-strand	426-428	3	9
β-strand	431-436	6	3
β-strand	443	1	10
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	10
α-helix	481-494	14
α-helix	511-517	7
α-helix	520-529	10

Chains B and D: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	11
α-helix	18-21	4
α-helix	28-29	2
α-helix	30-47	18
β-strand	53-59	7	11
β-strand	65	1	11
β-strand	70	1	12
β-strand	73	1	12
β-strand	77-84	8	11
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	127-135	9	11
α-helix	147-156	10
β-strand	159-165	7	11
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	11
α-helix	227-231	5
α-helix	241-245	5
β-strand	247-252	6	10
β-strand	259-268	10	10
β-strand	277-280	4	7
β-strand	289-297	9	6
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	10
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	10
α-helix	367	1
α-helix	371-386	16
β-strand	389-396	8	10
α-helix	402-403	2
β-strand	404-412	9	10
β-strand	417-423	7	10
β-strand	430	1	4
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	3
β-strand	464-466	3	13
β-strand	473-475	3	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	8

Chain C: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	37-43	7	14
α-helix	46-49	4
α-helix	57-58	2
α-helix	59-76	18
β-strand	82-88	7	14
β-strand	94	1	14
β-strand	102-109	8	14
α-helix	113-120	8
α-helix	125-134	10
α-helix	143-153	11
α-helix	154-156	3
β-strand	164-170	7	14
α-helix	180-196	17
β-strand	198-204	7	14
β-strand	205	1	15
α-helix	233-235	3
β-strand	236	1	15
α-helix	239-250	12
β-strand	257-262	6	16
β-strand	268-274	7	16
β-strand	277	1	17
α-helix	282-285	4
β-strand	286-289	4	18
β-strand	296-304	9	19
α-helix	309	1
β-strand	310	1	19
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	20
β-strand	325-329	5	20
α-helix	331-336	6
β-strand	344-352	9	16
α-helix	353-355	3
β-strand	366-370	5	16
β-strand	375-376	2	21
α-helix	378-392	15
β-strand	394-401	8	16
β-strand	409-416	8	16
α-helix	417-418	2
β-strand	419-420	2	22
β-strand	426-428	3	22
β-strand	431-436	6	16
α-helix	437-439	3
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 E: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	37-43	7	27
α-helix	46-49	4
α-helix	57-58	2
α-helix	59-76	18
β-strand	82-88	7	27
β-strand	94	1	27
β-strand	102-109	8	27
α-helix	113-120	8
α-helix	125-134	10
α-helix	143-153	11
α-helix	154-157	4
β-strand	164-170	7	27
α-helix	180-196	17
β-strand	198-204	7	27
β-strand	205	1	28
α-helix	233-235	3
β-strand	236	1	28
α-helix	239-250	12
β-strand	257-262	6	29
β-strand	268-274	7	29
β-strand	277	1	30
α-helix	282-285	4
β-strand	286-289	4	31
β-strand	296-304	9	32
α-helix	313-315	3
β-strand	316-322	7	33
β-strand	325-329	5	33
α-helix	331-336	6
β-strand	344-352	9	29
α-helix	353-355	3
β-strand	366-370	5	29
β-strand	375-376	2	34
α-helix	378-392	15
β-strand	394-401	8	29
β-strand	409-416	8	29
β-strand	419-420	2	35
β-strand	426-428	3	35
β-strand	431-436	6	29
β-strand	443	1	36
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 F: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	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
β-strand	70	1	38
β-strand	73	1	38
β-strand	77-84	8	37
α-helix	88-92	5
α-helix	93-97	5
α-helix	107-121	15
β-strand	127-135	9	37
α-helix	147-156	10
β-strand	159-165	7	37
α-helix	196-198	3
α-helix	199-216	18
α-helix	218-223	6
β-strand	224-226	3	37
α-helix	227-231	5
α-helix	241-245	5
β-strand	247-253	7	36
β-strand	257-268	12	36
β-strand	277-280	4	33
β-strand	289-297	9	32
β-strand	304	1	32
α-helix	305-306	2
β-strand	310-316	7	31
β-strand	319-322	4	31
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	371-386	16
β-strand	389-396	8	36
α-helix	402-403	2
β-strand	404-412	9	36
β-strand	417-423	7	36
β-strand	430	1	30
α-helix	435-437	3
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	29
β-strand	464-466	3	39
β-strand	473-475	3	39
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	520-525	6
α-helix	527-536	10
β-strand	540-541	2	34

Chain G: 22 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	37-43	7	40
α-helix	46-49	4
α-helix	57-58	2
α-helix	59-76	18
β-strand	82-88	7	40
β-strand	94	1	40
β-strand	102-109	8	40
α-helix	113-120	8
α-helix	125-134	10
α-helix	143-153	11
β-strand	164-170	7	40
α-helix	180-196	17
β-strand	198-204	7	40
β-strand	205	1	41
α-helix	233-235	3
β-strand	236	1	41
α-helix	239-250	12
β-strand	257-262	6	42
β-strand	268-274	7	42
β-strand	277	1	43
α-helix	282-285	4
β-strand	286-289	4	44
β-strand	296-304	9	45
α-helix	309	1
β-strand	310	1	45
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	46
β-strand	325-329	5	46
α-helix	331-336	6
β-strand	344-352	9	42
α-helix	353-355	3
β-strand	366-370	5	42
β-strand	375-376	2	47
α-helix	378-392	15
β-strand	394-401	8	42
β-strand	409-416	8	42
β-strand	419-420	2	48
β-strand	426-428	3	48
β-strand	431-436	6	42
β-strand	443	1	49
α-helix	444-445	2
α-helix	453-455	3
α-helix	456-468	13
β-strand	470	1	49
α-helix	481-494	14
α-helix	511-517	7
α-helix	520-529	10

Chain H: 26 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	50
α-helix	18-20	3
α-helix	28-29	2
α-helix	30-47	18
β-strand	53-59	7	50
β-strand	65	1	50
β-strand	70	1	51
β-strand	73	1	51
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	147-156	10
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	247-252	6	49
β-strand	259-268	10	49
β-strand	277-280	4	46
β-strand	289-297	9	45
β-strand	304	1	45
α-helix	305-306	2
β-strand	310-316	7	44
β-strand	319-322	4	44
α-helix	325-331	7
β-strand	339-347	9	49
α-helix	348-350	3
α-helix	353-355	3
β-strand	357-366	10	49
α-helix	367	1
α-helix	371-386	16
β-strand	389-396	8	49
α-helix	402-403	2
β-strand	404-412	9	49
β-strand	417-423	7	49
β-strand	430	1	43
α-helix	445-447	3
α-helix	448-460	13
β-strand	462	1	42
β-strand	464-466	3	52
β-strand	473-475	3	52
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	47

Chains Q, R, S and T: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	181-183	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
X-ray repair cross-complementing protein 6	A, C, E, G	protein	544	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B, D, F, H	protein	572	Homo sapiens	P13010 (AlphaFold model)
DNA (5'-d(gptptptptptpapgptptptpaptptpgpgpgpcpgpcp*g)-3')	I, K, M, O	DNA	21	synthetic construct
DNA (34-mer)	J, L, N, P	DNA	34	synthetic construct
Aprataxin and PNK-like factor	Q, R, S, T	protein	18	Homo sapiens	Q8IW19 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6ERF_1 X-ray repair cross-complementing protein 6 (chains A, C, E, G)
MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPF
DMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELD
QFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDS
AKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLE
DLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKT
RTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHH
YLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEEL
DDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFEN
PVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKV
TKRK

Sequence of entity 2 (B, D, F, H), FASTA

>6ERF_2 X-ray repair cross-complementing protein 5 (chains B, D, F, H)
MHHHHHHHHHHENLYFQGVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQ
RQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQ
QADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQF
FLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDE
IYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKT
LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL
GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANP
QVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSL
AKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVT
TKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQ

Sequence of entity 3 (I, K, M, O), FASTA

>6ERF_3 DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3') (chains I, K, M, O)
GTTTTTAGTTTATTGGGCGCG

Sequence of entity 4 (J, L, N, P), FASTA

>6ERF_4 DNA (34-MER) (chains J, L, N, P)
CGCGCCCAGCTTTCCCAGCTAATAAACTAAAAAC

Sequence of entity 5 (Q, R, S, T), FASTA

>6ERF_5 Aprataxin and PNK-like factor (chains Q, R, S, T)
KQQPILAERKRILPTWML

Primary citation

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nemoz, C., Ropars, V., Frit, P. et al. Nat Struct Mol Biol (2018) 25:971-980. DOI 10.1038/s41594-018-0133-6 · 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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