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8gkh

Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with omega RNA and target DNA

Method: ELECTRON MICROSCOPY Dmax: 122.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing protein

Spizellomyces punctatus

UniProt A0A0F8NYV9

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 Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain P； UniProt 1–369 Not recorded ;DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') ; × 1 DNA (35-MER) × 1 RNA (78-MER) × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.70 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.

Other PDB Difference from Current Entry 8GKH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
28QN MBP-maltose bound to distal DARPin (AHIR dodecamer scaffold system) Deposited 2026-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–374（374 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5T6R Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex Deposited 2016-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 45-meric
Chain V 1–383（383 aa）
Not recorded MG MAGNESIUM ION × 86 K POTASSIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6GFJ Structure of RIP2 CARD domain fused to crystallisable MBP tag Deposited 2018-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–371（371 aa）
Chain B 1–371（371 aa）
Chain C 1–371（371 aa）
Chain D 1–371（371 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M NaNO3, and 22% (w/v) PEG 3350
Resolution 3.30 Å R-free 0.266
6XDS Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol Deposited 2020-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–368（367 aa）
Not recorded V5S 2-[(4-bromophenyl)amino]ethan-1-ol × 1 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；100 mM BisTris pH 5.5, 100 mM ammonium acetate, 15% PEG4000, 15% glycerol
Resolution 1.47 Å R-free 0.208

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0F8NYV9_METMZ
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 18–386； UniProt 1–369

Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing protein

Spizellomyces punctatus

UniProt A0A0L0H5U9

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 Monomer Protein × 1 DNA 2 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain P； UniProt 2–638 Not recorded ;DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') ; × 1 DNA (35-MER) × 1 RNA (78-MER) × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 2.70 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.

Other PDB Difference from Current Entry 8GKH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9CEU Spizellomyces punctatus Fanzor (SpuFz) State 1 Deposited 2024-06-27 Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric
Chain P 2–638（637 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.29 Å
9CEV Spizellomyces punctatus Fanzor (SpuFz) State 2 Deposited 2024-06-27 Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric
Chain P 2–638（637 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.26 Å
9CEW Spizellomyces punctatus Fanzor (SpuFz) State 3 Deposited 2024-06-27 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: hexameric
Chain P 2–638（637 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.88 Å
9CEX Spizellomyces punctatus Fanzor (SpuFz) State 4 Deposited 2024-06-27 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: hexameric
Chain P 2–638（637 aa）
Not recorded ZN ZINC ION × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
9CEY Spizellomyces punctatus Fanzor (SpuFz) State 5 Deposited 2024-06-27 Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric
Chain P 2–638（637 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.22 Å
9CEZ Spizellomyces punctatus Fanzor (SpuFz) State 6 Deposited 2024-06-27 Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric
Chain P 2–638（637 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.41 Å

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

View Construct and Data Evidence
UniProt name A0A0L0H5U9_SPIPD
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 396–1032； UniProt 2–638

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 8gkh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8gkh
Deposition date deposition_date2023-03-19
Structure title titleStructure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with omega RNA and target DNA
Keywords keywordsFanzor, Eukaryotic, RNA-guided, nuclease, Gene editing, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.62 Å
Radius of gyration Rg (electron density) rg_electron32.45 Å
Forward intensity I(0) i0298347000.00
Molecular weight molecular_weight110100.0 kDa
Excluded volume excluded_volume125490 ų
Envelope volume envelope_volume177200 ų
Hydration-shell volume shell_volume45596 ų
Envelope diameter envelope_diameter130.9 Å
Shell Rg shell_rg39.16 Å
Envelope Rg envelope_rg32.96 Å
Shape Rg shape_rg32.38 Å
Total Rg total_rg33.05 Å
Total atoms total_atoms7567
Residues n_residues725
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 dmax122.3 Å
Rg (real space) rg_real33.70 Å
Rg uncertainty (real space) rg_real_error1.14 Å
I(0) (real space) i0_real2.9830e+08
I(0) uncertainty (real space) i0_real_error5.0850e+06
Rg (reciprocal space) rg_reciprocal33.65 Å
I(0) (reciprocal space) i0_reciprocal298300000.0000
Solution quality estimate total_estimate0.8390
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.0 Å
Skewness Skewness skewness0.509
Kurtosis Kurtosis kurtosis0.095
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha32720000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.974
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)