6X0M: Histone PARylation factor 1

Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin. Determined by electron microscopy at 6.3 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 6.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 12,421
Mol. weight: 421.55 kDa
Released: 16 Sept 2020

Explore 6X0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X0M contains 64 α-helices and 58 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 o: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	38-45	8
β-strand	79-80	2	7
α-helix	83-87	5
β-strand	115-120	6	7
β-strand	127-132	6	7
β-strand	142-147	6	7
α-helix	153-154	2
β-strand	155-156	2	7
α-helix	161-168	8
α-helix	208-215	8
α-helix	245-256	12
α-helix	261-267	7
α-helix	269-283	15
α-helix	288-300	13
α-helix	303-305	3
α-helix	306-319	14
α-helix	323-334	12

Chain O: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	39-45	7
β-strand	79-80	2	1
α-helix	83-87	5
α-helix	102-104	3
β-strand	115-120	6	1
β-strand	127-132	6	1
β-strand	142-147	6	1
β-strand	155-156	2	1
α-helix	161-171	11
α-helix	208-215	8
α-helix	245-256	12
α-helix	261-267	7
α-helix	269-283	15
α-helix	287-300	14
α-helix	303-305	3
α-helix	306-319	14
α-helix	323-334	12

Chain p: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	80-82	3
β-strand	92-94	3	8
β-strand	96-97	2	9
β-strand	100-101	2	9
β-strand	103-110	8	8
β-strand	115-126	12	8
β-strand	132-139	8	8
β-strand	146-151	6	8
α-helix	156-171	16
β-strand	189-191	3	8
α-helix	223-232	10
α-helix	235-243	9
α-helix	244-248	5
α-helix	259-277	19
α-helix	283-295	13
α-helix	304-307	4
α-helix	311-333	23
α-helix	344-352	9
β-strand	354-358	5	10
α-helix	364-375	12
α-helix	379-381	3
β-strand	384-396	13	10
α-helix	399-402	4
β-strand	410-415	6	10
α-helix	422-428	7
α-helix	432-434	3
α-helix	439-441	3
β-strand	443	1	11
β-strand	445	1	11
β-strand	448-451	4	10
α-helix	454-458	5
α-helix	459-461	3
β-strand	469-478	10	10
β-strand	482-485	4	10
α-helix	490-493	4
β-strand	501-504	4	10
β-strand	506-510	5	12
α-helix	512-514	3
β-strand	516-518	3	10
β-strand	521-523	3	10
β-strand	528-530	3	12
β-strand	541-543	3	12
β-strand	545-548	4	10
α-helix	551-553	3
β-strand	554-566	13	10

Chain P: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	80-82	3
β-strand	92-94	3	2
β-strand	96-97	2	3
β-strand	100-101	2	3
β-strand	103-110	8	2
β-strand	115-126	12	2
β-strand	132-139	8	2
β-strand	146-151	6	2
α-helix	156-171	16
β-strand	189-191	3	2
α-helix	223-233	11
α-helix	235-243	9
α-helix	244-248	5
α-helix	259-277	19
α-helix	283-295	13
α-helix	304-307	4
α-helix	311-333	23
α-helix	344-352	9
β-strand	355-358	4	4
α-helix	364-375	12
β-strand	384-395	12	4
α-helix	399-402	4
β-strand	410-416	7	4
α-helix	422-428	7
α-helix	432-434	3
α-helix	439-441	3
β-strand	443	1	5
β-strand	445	1	5
β-strand	448-451	4	4
α-helix	454-458	5
α-helix	459-461	3
β-strand	469-478	10	4
β-strand	482-485	4	4
β-strand	501-504	4	4
β-strand	506-510	5	6
α-helix	512-514	3
β-strand	516-518	3	4
β-strand	521-523	3	4
β-strand	528-530	3	6
β-strand	541-543	3	6
β-strand	545-548	4	4
α-helix	551-553	3
β-strand	554-566	13	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone PARylation factor 1	O, o	protein	356	Homo sapiens	Q9NWY4 (AlphaFold model)
Poly [ADP-ribose] polymerase 2	P, p	protein	590	Homo sapiens	Q9UGN5 (AlphaFold model)
DNA (167-mer)	I, i	DNA	167	synthetic construct
DNA (167-mer)	J, j	DNA	167	synthetic construct

Sequence of entity 1 (O, o), FASTA

>6X0M_1 Histone PARylation factor 1 (chains O, o)
MGHHHHHHGGMVGGGGKRRPGGEGPQCEKTTDVKKSKFCEADVSSDLRKEVENHYKLSLP
EDFYHFWKFCEELDPEKPSDSLSASLGLQLVGPYDILAGKHKTKKKSTGLNFNLHWRFYY
DPPEFQTIIIGDNKTQYHMGYFRDSPDEFPVYVGINEAKKNCIIVPNGDNVFAAVKLFLT
KKLKEITDKKKINLLKNIDEKLTEAARELGYSLEQRTVKMKQRDKKVVTKTFHGAGLVVP
VDKNDVGYRELPETDADLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFANDECDYGMG
LELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEEHLANRSQENIDQLAA

Sequence of entity 2 (P, p), FASTA

>6X0M_2 Poly [ADP-ribose] polymerase 2 (chains P, p)
MGSSHHHHHHSSGLVPRGSHMAARRRRSTGGGRARALNESKRVNNGNTAPEDSSPAKKTR
RCQRQESKKMPVAGGKANKDRTEDKQDESVKALLLKGKAPVDPECTAKVGKAHVYCEGND
VYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSVWMRWGRVGKMGQHSLVACSGNLNKAK
EIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMDYATNTQDEEETKKEESLKSPLKPESQ
LDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQ
HGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQS
PEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEK
EAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANY
CFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNG
STVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW

Sequence of entity 3 (I, i), FASTA

>6X0M_3 DNA (167-MER) (chains I, i)
CAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCATCATAG

Sequence of entity 4 (J, j), FASTA

>6X0M_4 DNA (167-MER) (chains J, j)
CTATGATGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTG

Primary citation

Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin. Bilokapic, S., Suskiewicz, M.J., Ahel, I. et al. Nature (2020) 585:609-613. DOI 10.1038/s41586-020-2725-7 · PubMed

Other PDB entries of the same protein (UniProt Q9NWY4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6M3G 1.57 Å, Crystal structure of human HPF1
6M3I 1.98 Å, Crystal structure of HPF1/PARP1 complex
6TX2 2.09 Å, Human HPF1
6TX3 2.96 Å, HPF1 bound to catalytic fragment of PARP2
6X0L 3.9 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
9MJA 4.3 Å, PARP1 ART in complex with HPF1 and EB47
6X0N 10.0 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin

Browse structure collections

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