6uro

Cryo-EM structure of human CPSF160-WDR33-CPSF30-PAS RNA-CstF77 complex

Method: ELECTRON MICROSCOPY Dmax: 190.5 Å Quality: GOOD

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

Cleavage and polyadenylation specificity factor subunit 1

Homo sapiens

UniProt Q10570

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–RNA Heteromer Protein × 5 RNA 1 PDB declaration: hexameric(6) Consistent with all polymer counts Chain A; UniProt 1–1443 Not recorded ;pre-mRNA 3' end processing protein WDR33 ; × 1 (Q9C0J8) Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) PAS RNA × 1 Cleavage stimulation factor subunit 3 × 2 (Q12996) ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 Å

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPSF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1443; UniProt 1–1443

;pre-mRNA 3' end processing protein WDR33 ;

Homo sapiens

UniProt Q9C0J8

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–RNA Heteromer Protein × 5 RNA 1 PDB declaration: hexameric(6) Consistent with all polymer counts Chain B; UniProt 1–572 Not recorded Cleavage and polyadenylation specificity factor subunit 1 × 1 (Q10570) Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) PAS RNA × 1 Cleavage stimulation factor subunit 3 × 2 (Q12996) ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 Å

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WDR33_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 16–587; UniProt 1–572

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–RNA Heteromer Protein × 5 RNA 1 PDB declaration: hexameric(6) Consistent with all polymer counts Chain C; UniProt 1–244 Not recorded Cleavage and polyadenylation specificity factor subunit 1 × 1 (Q10570) ;pre-mRNA 3' end processing protein WDR33 ; × 1 (Q9C0J8) PAS RNA × 1 Cleavage stimulation factor subunit 3 × 2 (Q12996) ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 Å

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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPSF4_HUMAN
Isoform O95639-2
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–244; UniProt 1–244

Cleavage stimulation factor subunit 3

Homo sapiens

UniProt Q12996

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–RNA Heteromer Protein × 5 RNA 1 PDB declaration: hexameric(6) Consistent with all polymer counts Chain E; UniProt 1–717 Chain F; UniProt 1–717 Not recorded Cleavage and polyadenylation specificity factor subunit 1 × 1 (Q10570) ;pre-mRNA 3' end processing protein WDR33 ; × 1 (Q9C0J8) Cleavage and polyadenylation specificity factor subunit 4 × 1 (O95639) PAS RNA × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM DTT cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 Å

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSTF3_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–717; UniProt 1–717 Author chain F; PDBConstruct 1–717; UniProt 1–717

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 6uro

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6uro
Deposition date deposition_date2019-10-23
Structure title titleCryo-EM structure of human CPSF160-WDR33-CPSF30-PAS RNA-CstF77 complex
Keywords keywords;pre-mRNA 3'-end processing, RNA binding, AAUAAA polyadenylation signal, RNA BINDING PROTEIN-RNA complex, mPSF ;; RNA BINDING PROTEIN/RNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier54.06
Radius of gyration Rg (electron density) rg_electron54.25
Forward intensity I(0) i01418720000.00
Molecular weight molecular_weight318490.0 kDa
Excluded volume excluded_volume400060 ų
Envelope volume envelope_volume560570 ų
Hydration-shell volume shell_volume88166 ų
Envelope diameter envelope_diameter200.6
Shell Rg shell_rg54.54
Envelope Rg envelope_rg55.15
Shape Rg shape_rg54.23
Total Rg total_rg54.34
Total atoms total_atoms22401
Residues n_residues2755
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 dmax190.5
Rg (real space) rg_real54.36
Rg uncertainty (real space) rg_real_error2.15
I(0) (real space) i0_real1.4190e+09
I(0) uncertainty (real space) i0_real_error2.9300e+07
Rg (reciprocal space) rg_reciprocal53.80
I(0) (reciprocal space) i0_reciprocal1418000000.0000
Solution quality estimate total_estimate0.8393
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.5
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.294
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha199200000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.648

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id6uroA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6uroE01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id6uroE02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id6uroF01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain
Domain ID domain_id6uroF02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily10 — Tetratricopeptide repeat domain

8. Citations (1)

9. Files and Curves (10)