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8t1q

Crystal structure of human CPSF73 catalytic segment in complex with compound 1

Method: X-RAY DIFFRACTION Dmax: 82.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cleavage and polyadenylation specificity factor subunit 3

Homo sapiens

UniProt Q9UKF6

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 1–459 Not recorded XYX 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(4-ethanoylphenyl)phenyl]propanamide × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 FE FE (III) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7 Resolution 1.70 Å R-free 0.215

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 8T1Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2I7T Structure of human CPSF-73 Deposited 2006-08-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100mM MOPS (pH 6.5), 16% PEG 3350, 300mM sodium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.10 Å R-free 0.276
2I7V Structure of Human CPSF-73 Deposited 2006-08-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；100mM MOPS (pH 6.5), 300mM sodium sulfate, 16% PEG 3350, 0.5mM Zinc Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.10 Å R-free 0.252
6M8Q Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531 Deposited 2018-08-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Not recorded ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting.
Resolution 2.49 Å R-free 0.221
6M8Q Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531 Deposited 2018-08-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–459（459 aa）
Not recorded ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting.
Resolution 2.49 Å R-free 0.221
6V4X Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution Deposited 2019-12-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain H 1–684（684 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T1R Crystal structure of human CPSF73 catalytic segment in complex with compound 2 Deposited 2023-06-02 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–459（459 aa）
Not recorded XZC 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(3-methoxyphenyl)phenyl]propanamide × 1 FE FE (III) ION × 2 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7
Resolution 2.20 Å R-free 0.250
9NB1 CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73 Deposited 2025-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain H 1–684（684 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.85 Å
9NGO CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (FOCUS MAP) Deposited 2025-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–684（684 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9NH5 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (core region) Deposited 2025-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain H 1–684（684 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
9NH6 CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA (COMPOSITE MAP) Deposited 2025-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain H 1–684（684 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPSF3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–479； UniProt 1–459

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 8t1q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t1q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t1q
Deposition date deposition_date2023-06-02
Structure title titleCrystal structure of human CPSF73 catalytic segment in complex with compound 1
Keywords keywordsnuclease, complex, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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_guinier23.57 Å
Radius of gyration Rg (electron density) rg_electron22.48 Å
Forward intensity I(0) i041167400.00
Molecular weight molecular_weight49960.0 kDa
Excluded volume excluded_volume62588 ų
Envelope volume envelope_volume72795 ų
Hydration-shell volume shell_volume26769 ų
Envelope diameter envelope_diameter85.5 Å
Shell Rg shell_rg29.96 Å
Envelope Rg envelope_rg22.97 Å
Shape Rg shape_rg22.49 Å
Total Rg total_rg23.33 Å
Total atoms total_atoms3506
Residues n_residues433
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 dmax82.8 Å
Rg (real space) rg_real23.55 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real4.1170e+07
I(0) uncertainty (real space) i0_real_error6.1060e+05
Rg (reciprocal space) rg_reciprocal23.56 Å
I(0) (reciprocal space) i0_reciprocal41170000.0000
Solution quality estimate total_estimate0.8493
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.089
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12840000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.694; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)