8AG5: Vaccinia C16 protein

Vaccinia C16 protein bound to Ku70/Ku80. Determined by electron microscopy at 3.47 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 3.47 Å
Organisms: Homo sapiens, Vaccinia virus Western Reserve
Chains: 4
Atoms: 13,762
Mol. weight: 244.73 kDa
Released: 9 Nov 2022

Explore 8AG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AG5 contains 65 α-helices and 102 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: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	36-43	8	1
α-helix	46-49	4
α-helix	59-77	19
β-strand	82-88	7	1
β-strand	102-109	8	1
α-helix	113-120	8
α-helix	124-134	11
α-helix	143-155	13
β-strand	162-169	8	1
α-helix	180-196	17
β-strand	199-202	4	1
β-strand	205	1	2
α-helix	213-216	4
α-helix	232-235	4
β-strand	236	1	2
α-helix	239-250	12
α-helix	251-253	3
β-strand	257	1	3
β-strand	260-262	3	3
β-strand	268-274	7	3
β-strand	277	1	4
α-helix	279-285	7
β-strand	286	1	5
β-strand	288	1	6
β-strand	295	1	6
β-strand	299-303	5	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	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	394-401	8	3
β-strand	409-416	8	3
β-strand	419-420	2	10
β-strand	426-428	3	10
β-strand	431-436	6	3
α-helix	440-442	3
β-strand	443	1	11
α-helix	444-448	5
α-helix	456-468	13
β-strand	470	1	11
α-helix	481-494	14
α-helix	499-502	4
α-helix	511-518	8
α-helix	521-529	9

Chain B: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	8-15	8	13
β-strand	24	1	14
β-strand	27	1	14
α-helix	30-47	18
β-strand	53-59	7	13
β-strand	65	1	13
β-strand	77-84	8	13
α-helix	88-96	9
α-helix	107-121	15
β-strand	129-135	7	13
α-helix	147-156	10
β-strand	159-165	7	13
α-helix	199-215	17
α-helix	218-223	6
β-strand	224-226	3	13
α-helix	227-230	4
α-helix	235-237	3
α-helix	243	1
β-strand	244	1	12
α-helix	245-246	2
β-strand	247-252	6	11
β-strand	258-267	10	11
α-helix	276	1
β-strand	277-280	4	8
α-helix	286-288	3
β-strand	290-294	5	7
β-strand	313-315	3	5
β-strand	320-322	3	5
α-helix	323-325	3
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
α-helix	427-429	3
β-strand	430	1	4
α-helix	448-460	13
β-strand	462	1	3
β-strand	464-466	3	15
β-strand	473-475	3	15
α-helix	479-481	3
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: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
β-strand	10-15	6	16
α-helix	23-29	7
β-strand	38-41	4	16
α-helix	48-59	12
β-strand	66-69	4	16
β-strand	73-78	6	16
β-strand	85-86	2	17
β-strand	98-108	11	16
β-strand	113	1	18
β-strand	116-119	4	17
β-strand	124-127	4	17
β-strand	130-134	5	16
β-strand	138-141	4	17
α-helix	142-143	2
β-strand	144	1	18
β-strand	149-159	11	16
β-strand	165-167	3	19
β-strand	175-177	3	19
β-strand	178	1	20
β-strand	186-193	8	20
β-strand	203-208	6	20
β-strand	214-218	5	20
α-helix	224-228	5
β-strand	231-232	2	20
α-helix	235-238	4
α-helix	239-243	5
α-helix	247-250	4
β-strand	255-256	2	20
α-helix	268-273	6
α-helix	283-297	15
β-strand	304-310	7	20
β-strand	316-327	12	20

Chain D: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
β-strand	10-15	6	16
α-helix	23-30	8
β-strand	38-42	5	16
α-helix	48-60	13
β-strand	64-69	6	16
β-strand	72-78	7	16
β-strand	84	1	17
β-strand	98-108	11	16
β-strand	116-118	3	17
β-strand	124-127	4	17
β-strand	130-134	5	16
β-strand	139-141	3	17
β-strand	149-160	12	16
β-strand	164-168	5	21
β-strand	174-178	5	21
β-strand	186-193	8	21
α-helix	194-195	2
β-strand	199	1	22
β-strand	203-209	7	21
β-strand	214-218	5	21
α-helix	224-227	4
β-strand	231-232	2	21
α-helix	235-242	8
β-strand	244	1	22
β-strand	255-256	2	21
α-helix	282-298	17
β-strand	304-310	7	21
β-strand	313	1	12
α-helix	315	1
β-strand	316-327	12	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ku70-Xrcc6	A	protein	651	Homo sapiens	P12956 (AlphaFold model)
X-ray repair cross-complementing protein 5	B	protein	755	Homo sapiens	P13010 (AlphaFold model)
Protein C10	C, D	protein	369	Vaccinia virus Western Reserve	P03296 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8AG5_1 Ku70-Xrcc6 (chains A)
MSAWSHPQFEKGSAGSAAGSGAGWSHPQFEKLEVLFQGPGGSMSGWESYYKTEGDEEAEE
EQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISS
DRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHG
SDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGI
FLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSR
LKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKR
SQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGS
STLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLP
FADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLM
EPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRKHDNEGSGSKRPKVE
YSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD

Sequence of entity 2 (B), FASTA

>8AG5_2 X-ray repair cross-complementing protein 5 (chains B)
MAHHHHHHHHHHGALEVLFQGPHMVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKV
ITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPDFDLLEDIESK
IQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKC
DISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEG
EDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWT
VVDAKTLKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEG
KCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAY
DKRANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDAL
IDSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLN
PPAEVTTKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPTAKKLKTEQGGAHFS
VSSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNETPYFMKSID
CIRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVT
AEEAKKFLAPKDKPSGDTAAVFEEGGDVDDLLDMI

Sequence of entity 3 (C, D), FASTA

>8AG5_3 Protein C10 (chains C, D)
MDIYDDKGLQTIKLFNNEFDCIRNDIRELFKHVTDSDSIQLPMEDNSDIIENIRKILYRR
LKNVECVDIDSTITFMKYDPNDDNKRTCSNWVPLTNNYMEYCLVIYLETPICGGKIKLYH
PTGNIKSDKDIMFAKTLDFKSKKVLTGRKTIAVLDISVSYNRSMTTIHYNDDVDIDIHTD
KNGKELCYCYITIDDHYLVDVETIGVIVNRSGKCLLVNNHLGIGIVKDKRISDSFGDVCM
DTIFDFSEARELFSLTNDDNRNIAWDTDKLDDDTDIWTPVTEDDYKFLSRLVLYAKSQSD
TVFDYYVLTGDTEPPTVFIFKVTRFYFNMPKGGENLYFQGWSHPQFEKGGGSGGGSGGSS
AWSHPQFEK

Primary citation

Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus. Rivera-Calzada, A., Arribas-Bosacoma, R., Ruiz-Ramos, A. et al. Nat Commun (2022) 13:7062-7062. DOI 10.1038/s41467-022-34843-z · 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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