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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "XRCC6"

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Search Summary

This query matches 32 Structures.

Refinements

Structure Determination Methodology

experimental (32)

Scientific Name of Source Organism

	Homo sapiens (32)
	synthetic construct (10)
	DNA molecule (1)
	Escherichia coli (1)
	Vaccinia virus Western Reserve (1)

Taxonomy

	Eukaryota (32)
	other sequences (10)
	Bacteria (1)
	Varidnaviria (1)
	unclassified sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (27)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

	Protein (32)
	DNA (29)

Refinement Resolution (Å)

	2.0 - 2.5 (1)
	2.5 - 3.0 (7)
	3.0 - 3.5 (5)
	3.5 - 4.0 (7)
	4.0 - 4.5 (3)
	> 4.5 (9)

Release Date

	2015 - 2019 (4)
	2020 - 2024 (27)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (32)
	Lyases (32)
	Transferases (20)
	Ligases (9)

Symmetry Type

	Asymmetric (26)
	Cyclic (6)

AllSelected

1 to 25 of 32 Structures

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5Y3R \| pdb_00005y3r	Download File View File

Cryo-EM structure of Human DNA-PK Holoenzyme

Yin, X., Liu, M., Tian, Y., Wang, J., Xu, Y.

(2017) Cell Res 27: 1341-1350

Released	2017-09-06
Method	ELECTRON MICROSCOPY 6.6 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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6ERF \| pdb_00006erf	Download File View File

Complex of APLF factor and Ku heterodimer bound to DNA

Nemoz, C., Legrand, P., Ropars, V., Charbonnier, J.B.

(2018) Nat Struct Mol Biol 25: 971-980

Released	2018-10-17
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Aprataxin and PNK-like factor (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (34-MER) (nucleic acid) DNA (5'-D(GPTPTPTPTPTPAPGPTPTPTPAPTPTPGPGPGPCPGPCP*G)-3') (nucleic acid)

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6ERG \| pdb_00006erg	Download File View File

Complex of XLF and heterodimer Ku bound to DNA

Nemoz, C., Legrand, P., Ropars, V., Charbonnier, J.B.

(2018) Nat Struct Mol Biol 25: 971-980

Released	2018-10-17
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Non-homologous end-joining factor 1 (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (21-MER) (nucleic acid) DNA (34-MER) (nucleic acid)
Unique Ligands	SO4

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6ERH \| pdb_00006erh	Download File View File

Complex of XLF and heterodimer Ku bound to DNA

Nemoz, C., Legrand, P., Ropars, V., Charbonnier, J.B.

(2018) Nat Struct Mol Biol 25: 971-980

Released	2018-10-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Non-homologous end-joining factor 1 (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (21-MER) (nucleic acid) DNA (34-MER) (nucleic acid)
Unique Ligands	SO4

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6ZHA \| pdb_00006zha	Download File View File

Cryo-EM structure of DNA-PK monomer

Chaplin, A.K., Hardwick, S.W., Chirgadze, D.Y., Blundell, T.L.

(2021) Nat Struct Mol Biol 28: 13-19

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.91 Å
Organisms	Homo sapiens
Macromolecule	DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-dependent protein kinase catalytic subunit,DNA-PKcs (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (nucleic acid)

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6ZHE \| pdb_00006zhe	Download File View File

Cryo-EM structure of DNA-PK dimer

Chaplin, A.K., Hardwick, S.W., Chirgadze, D.Y., Blundell, T.L.

(2021) Nat Struct Mol Biol 28: 13-19

Released	2020-10-21
Method	ELECTRON MICROSCOPY 7.24 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 4

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7AXZ \| pdb_00007axz	Download File View File

Ku70/80 complex apo form

Hnizda, A., Tesina, P., Novak, P., Blundell, T.L.

(2021) FEBS J 288: 4382-4393

Released	2021-02-10
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein)

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7K0Y \| pdb_00007k0y	Download File View File

Cryo-EM structure of activated-form DNA-PK (complex VI)

Chen, X., Gellert, M., Yang, W.

(2021) Mol Cell 81: 801-810.e3

Released	2021-01-06
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(APAPGPCPAPGPTPAPGPAPGPCPA)-3') (nucleic acid) DNA (5'-D(GPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCP*G)-3') (nucleic acid)

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7K1J \| pdb_00007k1j	Download File View File

CryoEM structure of inactivated-form DNA-PK (Complex III)

Chen, X., Gellert, M., Yang, W.

(2021) Mol Cell 81: 801-810.e3

Released	2021-01-06
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(APAPGPCPAPGPTPAPGPAPGPCPA)-3') (nucleic acid) DNA (5'-D(GPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCP*G)-3') (nucleic acid)

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7K1K \| pdb_00007k1k	Download File View File

CryoEM structure of inactivated-form DNA-PK (Complex IV)

Chen, X., Gellert, M., Yang, W.

(2021) Mol Cell 81: 801-810.e3

Released	2021-01-06
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(APAPGPCPAPGPTPAPGPAPGPCPA)-3') (nucleic acid) DNA (5'-D(GPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCP*G)-3') (nucleic acid)

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7K1N \| pdb_00007k1n	Download File View File

CryoEM structure of inactivated-form DNA-PK (Complex V)

Chen, X., Gellert, M., Yang, W.

(2021) Mol Cell 81: 801-810.e3

Released	2021-01-06
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(PAPAPGPCPAPGPTPAPGPAPGPCPA)-3') (nucleic acid) DNA (5'-D(PGPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCP*G)-3') (nucleic acid)

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7LSY \| pdb_00007lsy	Download File View File

NHEJ Short-range synaptic complex

He, Y., Chen, S.

(2021) Nature 593: 294-298

Released	2021-04-14
Method	ELECTRON MICROSCOPY 8.4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 5

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7LT3 \| pdb_00007lt3	Download File View File

NHEJ Long-range synaptic complex

He, Y., Chen, S.

(2021) Nature 593: 294-298

Released	2021-04-14
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	ADP

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7NFC \| pdb_00007nfc	Download File View File

Cryo-EM structure of NHEJ super-complex (dimer)

Chaplin, A.K., Hardwick, S.W., Kefala Stavridi, A., Chirgadze, D.Y., Blundell, T.L.

(2021) Mol Cell 81: 3400-3409

Released	2021-08-18
Method	ELECTRON MICROSCOPY 4.14 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 3

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7NFE \| pdb_00007nfe	Download File View File

Cryo-EM structure of NHEJ super-complex (monomer)

Chaplin, A.K., Hardwick, S.W., Kefala Stavridi, A., Chirgadze, D.Y., Blundell, T.L.

(2021) Mol Cell 81: 3400-3409

Released	2021-08-18
Method	ELECTRON MICROSCOPY 4.29 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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7SGL \| pdb_00007sgl	Download File View File

DNA-PK complex of DNA end processing

Liu, L., Li, J., Chen, X., Yang, W., Gellert, M.

(2022) Mol Cell 82: 177

Released	2022-01-12
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) Protein artemis (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) Hairpin_1 (nucleic acid)
Unique Ligands	ATP, IHP, MG, ZN

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7SU3 \| pdb_00007su3	Download File View File

CryoEM structure of DNA-PK complex VII

Chen, X., Liu, L., Gellert, M., Yang, W.

(2022) Mol Cell 82: 177

Released	2022-01-12
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(APAPGPCPAPGPTPAPGPAPG)-3') (nucleic acid) DNA (5'-D(GPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCP*G)-3') (nucleic acid)
Unique Ligands	ATP, IHP

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7Z6O \| pdb_00007z6o	Download File View File

X-Ray studies of Ku70/80 reveal the binding site for IP6

Varela, P.F., Charbonnier, J.B.

(2023) Nucleic Acids Res 51: 11732-11747

Released	2023-08-30
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(GPTPTPTPTPTPAPGPTPTPTPAPT)-3') (nucleic acid) DNA (5'-D(PAPAPAPTPAPAPAPCPTPAPAPAPAPAPC)-3') (nucleic acid)
Unique Ligands	IHP

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7Z87 \| pdb_00007z87	Download File View File

DNA-PK in the active state

Liang, S., Blundell, T.L.

(2023) Nat Struct Mol Biol 30: 140-147

Released	2023-01-18
Method	ELECTRON MICROSCOPY 2.91 Å
Organisms	Homo sapiens
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (26-MER) (nucleic acid)
Unique Ligands	1IX

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7Z88 \| pdb_00007z88	Download File View File

DNA-PK in the intermediate state

Liang, S., Blundell, T.L.

(2023) Nat Struct Mol Biol 30: 140-147

Released	2023-01-18
Method	ELECTRON MICROSCOPY 3.33 Å
Organisms	Homo sapiens
Macromolecule	DNA-dependent protein kinase catalytic subunit (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (26-MER) (nucleic acid)
Unique Ligands	1IX

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7ZT6 \| pdb_00007zt6	Download File View File

Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate

Kefala Stavridi, A., Chaplin, A.K., Blundell, T.L.

(2023) Nucleic Acids Res 51: 11732-11747

Released	2023-05-17
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein)
Unique Ligands	IHP

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7ZVT \| pdb_00007zvt	Download File View File

CryoEM structure of Ku heterodimer bound to DNA

Hardwick, S.W., Kefala-Stavridi, A., Chirgadze, D.Y., Blundell, T.L., Chaplin, A.K.

(2023) Nucleic Acids Res 51: 11732-11747

Released	2023-05-24
Method	ELECTRON MICROSCOPY 2.74 Å
Organisms	Homo sapiens
Macromolecule	X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(PCPGPAPTPAPTPCPTPAPGPAPGPGPGPAPT)-3') (nucleic acid) DNA (5'-D(PTPCPCPCPTPCPTPAPGPAPTPAPTPC)-3') (nucleic acid)
Unique Ligands	IHP

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7ZWA \| pdb_00007zwa	Download File View File

CryoEM structure of Ku heterodimer bound to DNA and PAXX

Hardwick, S.W., Kefala-Stavridi, A., Chirgadze, D.Y., Blundell, T.L., Chaplin, A.K.

(2023) Sci Adv 9: eadg2834-eadg2834

Released	2023-05-31
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Homo sapiens
Macromolecule	Protein PAXX (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein) DNA (5'-D(PCPGPAPTPAPTPCPTPAPGPAPGPGPGPAPTPC)-3') (nucleic acid) DNA (5'-D(PGPAPTPCPCPCPTPCPTPAPGPAPTPAPT)-3') (nucleic acid)
Unique Ligands	PO4

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7ZYG \| pdb_00007zyg	Download File View File

CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF

Hardwick, S.W., Kefala-Stavridi, A., Chirgadze, D.Y., Blundell, T.L., Chaplin, A.K.

(2023) Sci Adv 9: eadg2834-eadg2834

Released	2023-06-07
Method	ELECTRON MICROSCOPY 2.68 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	PO4

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8AG4 \| pdb_00008ag4	Download File View File

Vaccinia C16 protein bound to Ku70/Ku80

Rivera-Calzada, A., Arribas-Bosacoma, R., Pearl, L.H., Llorca, O.

(2022) Nat Commun 13: 7062-7062

Released	2022-11-09
Method	ELECTRON MICROSCOPY 2.46 Å
Organisms	Homo sapiens Vaccinia virus Western Reserve
Macromolecule	Protein C10 (protein) X-ray repair cross-complementing protein 5 (protein) X-ray repair cross-complementing protein 6 (protein)

1 to 25 of 32 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

5Y3R | pdb_00005y3r

6ERF | pdb_00006erf

6ERG | pdb_00006erg

6ERH | pdb_00006erh

6ZHA | pdb_00006zha

6ZHE | pdb_00006zhe

7AXZ | pdb_00007axz

7K0Y | pdb_00007k0y

7K1J | pdb_00007k1j

7K1K | pdb_00007k1k

7K1N | pdb_00007k1n

7LSY | pdb_00007lsy

7LT3 | pdb_00007lt3

7NFC | pdb_00007nfc

7NFE | pdb_00007nfe

7SGL | pdb_00007sgl

7SU3 | pdb_00007su3

7Z6O | pdb_00007z6o

7Z87 | pdb_00007z87

7Z88 | pdb_00007z88

7ZT6 | pdb_00007zt6

7ZVT | pdb_00007zvt

7ZWA | pdb_00007zwa

7ZYG | pdb_00007zyg

8AG4 | pdb_00008ag4