9cf0

Parasitella parasitica Fanzor (PpFz) State 1

Method: ELECTRON MICROSCOPY Dmax: 113.8 Å Quality: REASONABLE

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

Peptidyl-prolyl cis-trans isomerase

Saccharomyces cerevisiae

UniProt P14832

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 DNA 2 RNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain C; UniProt 1–162 Not recorded DNA non-target strand × 1 Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1 × 1 (P0AEX9,A0A0B7NJM7) DNA target strand × 1 Parasitella parasitica Fanzor 1 omegaRNA × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.47 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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYPH_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain C; PDBConstruct 1–162; UniProt 1–162

Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1

Parasitella parasitica

UniProt A0A0B7NJM7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 DNA 2 RNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain P; UniProt 2–849 Not recorded Peptidyl-prolyl cis-trans isomerase × 1 (P14832) DNA non-target strand × 1 DNA target strand × 1 Parasitella parasitica Fanzor 1 omegaRNA × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.47 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.

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

View Construct and Data Evidence
UniProt name A0A0B7NJM7_9FUNG
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 412–1259; UniProt 2–849

Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1

Parasitella parasitica

UniProt P0AEX9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 DNA 2 RNA 1 PDB declaration: pentameric(5) Consistent with all polymer counts Chain P; UniProt 27–392 Not recorded Peptidyl-prolyl cis-trans isomerase × 1 (P14832) DNA non-target strand × 1 DNA target strand × 1 Parasitella parasitica Fanzor 1 omegaRNA × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE-PROPANE Resolution 3.47 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.

366 other PDB entries and 491 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MALE_ECOLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain P; PDBConstruct 19–384; UniProt 27–392

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 9cf0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cf0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cf0
Deposition date deposition_date2024-06-27
Structure title titleParasitella parasitica Fanzor (PpFz) State 1
Keywords keywordsFanzor, Eukaryotic, RNA-guided, nuclease, Gene editing, RNA BINDING PROTEIN-ISOMERASE-DNA complex; RNA BINDING PROTEIN/ISOMERASE/DNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.27
Radius of gyration Rg (electron density) rg_electron35.00
Forward intensity I(0) i0311579000.00
Molecular weight molecular_weight127040.0 kDa
Excluded volume excluded_volume152550 ų
Envelope volume envelope_volume212690 ų
Hydration-shell volume shell_volume50729 ų
Envelope diameter envelope_diameter119.3
Shell Rg shell_rg41.41
Envelope Rg envelope_rg34.64
Shape Rg shape_rg35.00
Total Rg total_rg35.43
Total atoms total_atoms16982
Residues n_residues962
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 dmax113.8
Rg (real space) rg_real35.20
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real3.1160e+08
I(0) uncertainty (real space) i0_real_error4.8060e+06
Rg (reciprocal space) rg_reciprocal35.25
I(0) (reciprocal space) i0_reciprocal311600000.0000
Solution quality estimate total_estimate0.7101
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.0
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44680000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 1.000; Smooth: 0.924

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)