7zyh

Crystal structure of human CPSF30 in complex with hFip1

Method: X-RAY DIFFRACTION Dmax: 83.8 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cleavage and polyadenylation specificity factor subunit 4

Homo sapiens

UniProt O95639

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 118–178 Not recorded ;Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 ; × 2 (Q6UN15-4) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 118–178 Not recorded ;Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 ; × 2 (Q6UN15-4) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 118–178 Not recorded ;Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 ; × 2 (Q6UN15-4) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 118–178 Not recorded ;Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 ; × 2 (Q6UN15-4) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264

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.

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPSF4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–64; UniProt 118–178 Author chain D; PDBConstruct 4–64; UniProt 118–178 Author chain G; PDBConstruct 4–64; UniProt 118–178 Author chain J; PDBConstruct 4–64; UniProt 118–178

;Isoform 4 of Pre-mRNA 3'-end-processing factor FIP1 ;

Homo sapiens

UniProt Q6UN15-4

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 130–195 Chain C; UniProt 130–195 Not recorded Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 130–195 Chain F; UniProt 130–195 Not recorded Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 130–195 Chain I; UniProt 130–195 Not recorded Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 130–195 Chain L; UniProt 130–195 Not recorded Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;292.15 K;1.626 M (NH4)SO4, 0.1 M Bis-Tris pH 6.5 Resolution 2.20 Å R-free 0.264

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name FIP1-4_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–69; UniProt 130–195 Author chain C; PDBConstruct 4–69; UniProt 130–195 Author chain E; PDBConstruct 4–69; UniProt 130–195 Author chain F; PDBConstruct 4–69; UniProt 130–195 Author chain H; PDBConstruct 4–69; UniProt 130–195 Author chain I; PDBConstruct 4–69; UniProt 130–195 Author chain K; PDBConstruct 4–69; UniProt 130–195 Author chain L; PDBConstruct 4–69; UniProt 130–195

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 7zyh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7zyh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7zyh
Deposition date deposition_date2022-05-24
Structure title titleCrystal structure of human CPSF30 in complex with hFip1
Keywords keywords;Complex, 3' end processing, CPSF, GENE REGULATION ;; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.95
Radius of gyration Rg (electron density) rg_electron27.18
Forward intensity I(0) i077069800.00
Molecular weight molecular_weight66174.0 kDa
Excluded volume excluded_volume81690 ų
Envelope volume envelope_volume109410 ų
Hydration-shell volume shell_volume33568 ų
Envelope diameter envelope_diameter88.4
Shell Rg shell_rg34.61
Envelope Rg envelope_rg27.08
Shape Rg shape_rg27.16
Total Rg total_rg28.05
Total atoms total_atoms8977
Residues n_residues552
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.8
Rg (real space) rg_real27.74
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real7.7070e+07
I(0) uncertainty (real space) i0_real_error1.0240e+06
Rg (reciprocal space) rg_reciprocal27.81
I(0) (reciprocal space) i0_reciprocal77070000.0000
Solution quality estimate total_estimate0.9068
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.076
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8319000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.966

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)