7AXZ: Ku70/80 complex apo form

Ku70/80 complex apo form. Determined by electron microscopy at 3.2 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,225
Mol. weight: 152.76 kDa
Released: 10 Feb 2021

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

Secondary structure: helices and β-sheets

7AXZ contains 43 α-helices and 60 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: 22 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-43	8	1
α-helix	47-49	3
α-helix	57-58	2
α-helix	59-76	18
β-strand	82-88	7	1
β-strand	102-106	5	1
α-helix	113-120	8
α-helix	125-134	10
α-helix	143-156	14
β-strand	163-168	6	1
α-helix	180-195	16
β-strand	199-202	4	1
β-strand	205	1	2
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	283-285	3
β-strand	288-289	2	5
β-strand	301	1	6
β-strand	303	1	7
β-strand	304	1	8
α-helix	309	1
β-strand	310	1	7
α-helix	311-312	2
α-helix	313-315	3
β-strand	316-322	7	9
β-strand	325-329	5	9
α-helix	331-333	3
β-strand	344-349	6	3
β-strand	352	1	10
α-helix	353-355	3
β-strand	366-370	5	3
β-strand	375-376	2	11
α-helix	378-390	13
β-strand	394	1	10
β-strand	397-401	5	3
α-helix	407-408	2
β-strand	409-416	8	3
β-strand	420	1	12
β-strand	426	1	12
β-strand	431-437	7	3
α-helix	438	1
β-strand	443	1	13
α-helix	456-467	12
α-helix	481-493	13
α-helix	502-505	4
α-helix	511-518	8
α-helix	521-529	9

Chain B: 21 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	14
α-helix	18-21	4
α-helix	30-46	17
β-strand	53-59	7	14
β-strand	65	1	14
α-helix	70-72	3
β-strand	77-84	8	14
α-helix	88-93	6
α-helix	107-121	15
β-strand	129-130	2	14
β-strand	134-135	2	14
α-helix	147-157	11
β-strand	163-164	2	14
α-helix	199-216	18
α-helix	217-222	6
β-strand	224-225	2	14
α-helix	235-237	3
α-helix	241-243	3
β-strand	247-253	7	15
β-strand	257-265	9	15
β-strand	267	1	13
β-strand	277-280	4	9
β-strand	289	1	8
β-strand	292	1	6
β-strand	296	1	16
β-strand	304	1	16
β-strand	310-311	2	5
β-strand	313-316	4	17
β-strand	319-322	4	17
β-strand	339	1	18
β-strand	342	1	15
β-strand	346-347	2	19
β-strand	362-366	5	15
α-helix	367	1
α-helix	371-387	17
β-strand	389-390	2	19
β-strand	391-395	5	15
β-strand	396	1	18
β-strand	404-412	9	15
β-strand	417-423	7	15
β-strand	430	1	4
α-helix	435-437	3
α-helix	448-449	2
α-helix	450-454	5
α-helix	455-461	7
β-strand	464-466	3	20
β-strand	473-475	3	20
α-helix	483-484	2
α-helix	485-499	15
α-helix	504-509	6
α-helix	510-515	6
α-helix	520-536	17
β-strand	540-541	2	11

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)

Sequence of entity 1 (A), FASTA

>7AXZ_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

>7AXZ_2 X-ray repair cross-complementing protein 5 (chains B)
MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG
TDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQH
ETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGD
GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCVFKKI
ERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTLKKEDIQKETVYCLNDD
DETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQ
VLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECLV
YVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLFPTT
KIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLI
EAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFSVSSLAEGSVTSVGSVNPAENFRV
LVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFREEAIKFSEEQRFNNFLK
ALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLAPKDKPSGDTAAVFE
EGGDVDDLLDMI

Primary citation

SAP domain forms a flexible part of DNA aperture in Ku70/80. Hnizda, A., Tesina, P., Nguyen, T.B. et al. FEBS J (2021) 288:4382-4393. DOI 10.1111/febs.15732 · 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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