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8swy

PARP4 ART domain bound to NADH

Method: X-RAY DIFFRACTION Dmax: 120.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein mono-ADP-ribosyltransferase PARP4

Homo sapiens

UniProt Q9UKK3

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 242–282 Chain A； UniProt 365–573 Not recorded NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH Resolution 2.55 Å R-free 0.254
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 242–282 Chain B； UniProt 365–573 Not recorded NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH Resolution 2.55 Å R-free 0.254
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 242–282 Chain C； UniProt 365–573 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH Resolution 2.55 Å R-free 0.254

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 8SWY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11JF RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 1–1724（1724 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 242–282（41 aa）
Chain A 365–573（209 aa）
Not recorded GOL GLYCEROL × 1 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；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47
Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 242–282（41 aa）
Chain B 365–573（209 aa）
Not recorded GOL GLYCEROL × 1 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；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47
Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19 Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 242–282（41 aa）
Chain C 365–573（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47
Resolution 3.00 Å R-free 0.248
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 242–573（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5
Resolution 4.20 Å R-free 0.331
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 242–573（332 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；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47
Resolution 2.95 Å R-free 0.262
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 242–573（332 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；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47
Resolution 2.95 Å R-free 0.262
9BW6 Human Vault Cage in complex with PARP4 Deposited 2024-05-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric
Chain B 1–1724（1724 aa）
Chain D 1–1724（1724 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions
Resolution 2.90 Å
9BW6 Human Vault Cage in complex with PARP4 Deposited 2024-05-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1724（1724 aa）
Chain D 1–1724（1724 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions
Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric
Chain B 1–1724（1724 aa）
Chain D 1–1724（1724 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 78 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions
Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1724（1724 aa）
Chain D 1–1724（1724 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions
Resolution 2.90 Å
9DEV PARP4 BRCT domain Deposited 2024-08-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–100（100 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.15M Citric Acid pH3.5
Resolution 1.75 Å R-free 0.188
9DFO PARP4 BRCT domain K31Q mutant Deposited 2024-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–100（100 aa）
Mutation：K31Q SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；31% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6
Resolution 1.90 Å R-free 0.208
9DFP PARP4 BRCT domain K23/24Q mutant Deposited 2024-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–100（100 aa）
Mutation：K23Q,K24Q SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6
Resolution 1.92 Å R-free 0.219
9DFQ PARP4 BRCT domain F39Q mutant Deposited 2024-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–100（100 aa）
Mutation：F39Q SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 M ammonium sulfate and 0.1 M sodium acetate pH 4.6
Resolution 2.10 Å R-free 0.230
9DFR PARP4 BRCT domain F39A mutant Deposited 2024-08-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–100（100 aa）
Mutation：F39A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6
Resolution 1.90 Å R-free 0.218

11 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PARP4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–42； UniProt 242–282 Author chain A； PDBConstruct 51–259； UniProt 365–573 Author chain B； PDBConstruct 2–42； UniProt 242–282 Author chain B； PDBConstruct 51–259； UniProt 365–573 Author chain C； PDBConstruct 2–42； UniProt 242–282 Author chain C； PDBConstruct 51–259； UniProt 365–573

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 8swy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8swy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8swy
Deposition date deposition_date2023-05-19
Structure title titlePARP4 ART domain bound to NADH
Keywords keywordsPARP family, ADP-ribosyltransferase, marylation, vault, TRANSFERASE; TRANSFERASE
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_guinier33.83 Å
Radius of gyration Rg (electron density) rg_electron33.34 Å
Forward intensity I(0) i0110747000.00
Molecular weight molecular_weight82454.0 kDa
Excluded volume excluded_volume102800 ų
Envelope volume envelope_volume142600 ų
Hydration-shell volume shell_volume36085 ų
Envelope diameter envelope_diameter128.7 Å
Shell Rg shell_rg39.29 Å
Envelope Rg envelope_rg33.56 Å
Shape Rg shape_rg33.32 Å
Total Rg total_rg33.90 Å
Total atoms total_atoms5783
Residues n_residues724
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 dmax120.8 Å
Rg (real space) rg_real33.83 Å
Rg uncertainty (real space) rg_real_error1.39 Å
I(0) (real space) i0_real1.1070e+08
I(0) uncertainty (real space) i0_real_error1.9330e+06
Rg (reciprocal space) rg_reciprocal33.83 Å
I(0) (reciprocal space) i0_reciprocal110700000.0000
Solution quality estimate total_estimate0.6692
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.9 Å
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.367
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30270000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.860; Smooth: 0.938
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)