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6m3g

Crystal structure of human HPF1

Method: X-RAY DIFFRACTION Dmax: 69.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone PARylation factor 1

Homo sapiens

UniProt Q9NWY4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–346 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；300 K；0.1 M Tris-pH 8.1, 0.2 M potassium acetate, 20% w/v Polyethylene glycol (PEG) 3350 Resolution 1.57 Å R-free 0.205

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6M3G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6M3I Crystal structure of HPF1/PARP1 complex Deposited 2020-03-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–346（346 aa）
Not recorded UNU BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.1 M Tris-pH 7.0, 0.2 M magnesium formate dehydrate, 20% w/v PEG 3350.
Resolution 1.98 Å R-free 0.206
6TX2 Human HPF1 Deposited 2020-01-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 37–346（310 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；33% glycerol ethoxylate, 0.23 M lithium citrate tribasic tetrahydrate
Resolution 2.09 Å R-free 0.207
6TX3 HPF1 bound to catalytic fragment of PARP2 Deposited 2020-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–346（310 aa）
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6, 25% v/v pentaerythritol propoxylate (5/4 PO/OH)
Resolution 2.96 Å R-free 0.260
6X0L Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain O 1–346（346 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6X0M Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain O 1–346（346 aa）
Chain o 1–346（346 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain O 1–346（346 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
9MJA PARP1 ART in complex with HPF1 and EB47 Deposited 2024-12-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–346（346 aa）
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HPF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–346； UniProt 1–346

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6m3g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m3g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6m3g
Deposition date deposition_date2020-03-03
Structure title titleCrystal structure of human HPF1
Keywords keywordscofactor, ADP-ribosylation, DNA damage response, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.28 Å
Radius of gyration Rg (electron density) rg_electron20.30 Å
Forward intensity I(0) i020101000.00
Molecular weight molecular_weight34554.0 kDa
Excluded volume excluded_volume43486 ų
Envelope volume envelope_volume50325 ų
Hydration-shell volume shell_volume20982 ų
Envelope diameter envelope_diameter69.8 Å
Shell Rg shell_rg26.73 Å
Envelope Rg envelope_rg20.69 Å
Shape Rg shape_rg20.27 Å
Total Rg total_rg21.30 Å
Total atoms total_atoms2439
Residues n_residues303
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.7 Å
Rg (real space) rg_real21.26 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.0100e+07
I(0) uncertainty (real space) i0_real_error2.6850e+05
Rg (reciprocal space) rg_reciprocal21.26 Å
I(0) (reciprocal space) i0_reciprocal20100000.0000
Solution quality estimate total_estimate0.8856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5473000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)