6M3I: HPF1/PARP1 complex

Crystal structure of HPF1/PARP1 complex. Determined by X-ray diffraction at 1.98 Å resolution. Released 3 Mar 2021.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,702
Mol. weight: 67.67 kDa
Ligands: UNU
Released: 3 Mar 2021

Explore 6M3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M3I contains 29 α-helices and 24 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: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	51-63	13
α-helix	68-70	3
α-helix	73-76	4
β-strand	79-80	2	1
α-helix	83-87	5
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	161-173	13
α-helix	179-199	21
α-helix	208-214	7
β-strand	219	1	2
β-strand	227	1	2
α-helix	245-257	13
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	323-333	11

Chain B: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	667-676	10
α-helix	790-796	7
β-strand	799-803	5	3
α-helix	804-805	2
α-helix	809-820	12
β-strand	829-841	13	3
α-helix	844-848	5
α-helix	849-853	5
β-strand	857-864	8	3
α-helix	866-868	3
α-helix	869-875	7
β-strand	895-897	3	4
β-strand	898	1	3
α-helix	901-906	6
β-strand	911	1	5
β-strand	914	1	5
β-strand	916-925	10	3
β-strand	929-932	4	4
α-helix	941-942	2
β-strand	947-950	4	4
α-helix	951	1
β-strand	952-956	5	6
α-helix	958-960	3
β-strand	962-964	3	3
β-strand	967-969	3	3
α-helix	973	1
β-strand	974-976	3	6
β-strand	984-986	3	6
β-strand	988-991	4	4
α-helix	994-996	3
β-strand	997-1009	13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone PARylation factor 1	A	protein	346	Homo sapiens	Q9NWY4 (AlphaFold model)
Poly [ADP-ribose] polymerase 1	B	protein	253	Homo sapiens	P09874 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6M3I_1 Histone PARylation factor 1 (chains A)
MVGGGGKRRPGGEGPQCEKTTDVKKSKFCEADVSSDLRKEVENHYKLSLPEDFYHFWKFC
EELDPEKPSDSLSASLGLQLVGPYDILAGKHKTKKKSTGLNFNLHWRFYYDPPEFQTIII
GDNKTQYHMGYFRDSPDEFPVYVGINEAKKNCIIVPNGDNVFAAVKLFLTKKLREITDKK
KINLLKNIDEKLTEAARELGYSLEQRTVKMKQRDKKVVTKTFHGAGLVVPVDKNDVGYRE
LPETDADLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFANDECDYGMGLELGMDLFCY
GSHYFHKVAGQLLPLAYNLLKRNLFAEIIEEHLANRSQENIDQLAA

Sequence of entity 2 (B), FASTA

>6M3I_2 Poly [ADP-ribose] polymerase 1 (chains B)
GTKSKLPKPVQDLIKMIFGSGSGSGGDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNT
HATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAP
PEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKL
PKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKY
LLKLKFNFKTSLW

Ligands and cofactors

ID	Name	Formula	Copies
UNU	Benzamide	C7 H7 N O	1

Primary citation

HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones. Sun, F.H., Zhao, P., Zhang, N. et al. Nat Commun (2021) 12:1028-1028. DOI 10.1038/s41467-021-21302-4 · 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
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
6X0M 6.3 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
6X0N 10.0 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin

Browse structure collections

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