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- PDB-9cet: Guillardia theta Fanzor (GtFz) State 3 -

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Basic information

Entry
Database: PDB / ID: 9cet
TitleGuillardia theta Fanzor (GtFz) State 3
Components
  • DNA (28-MER)
  • DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*TP*AP*AP*AP*GP*GP*CP*CP*CP*CP*GP*GP*G)-3')
  • Maltose/maltodextrin-binding periplasmic protein,Guillardia theta Fanzor1
  • RNA (142-MER)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Fanzor / Eukaryotic / RNA-guided / nuclease / Gene editing / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Transposase IS605, OrfB, C-terminal / Putative transposase DNA-binding domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Cas12f1-like TNB domain-containing protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Guillardia theta (eukaryote)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsXu, P. / Saito, M. / Zhang, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2024
Title: Structural insights into the diversity and DNA cleavage mechanism of Fanzor.
Authors: Peiyu Xu / Makoto Saito / Guilhem Faure / Samantha Maguire / Samuel Chau-Duy-Tam Vo / Max E Wilkinson / Huihui Kuang / Bing Wang / William J Rice / Rhiannon K Macrae / Feng Zhang /
Abstract: Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different ...Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different organisms. We find that Fzs share a common ωRNA interaction interface, regardless of the length of the ωRNA, which varies considerably across species. The analysis also reveals Fz's mode of DNA recognition and unwinding capabilities as well as the presence of a non-canonical catalytic site. The structures demonstrate how protein conformations of Fz shift to allow the binding of double-stranded DNA to the active site within the R-loop. Mechanistically, examination of structures in different states shows that the conformation of the lid loop on the RuvC domain is controlled by the formation of the guide/DNA heteroduplex, regulating the activation of nuclease and DNA double-stranded displacement at the single cleavage site. Our findings clarify the mechanism of Fz, establishing a foundation for engineering efforts.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_software / entity / entity_poly / entity_poly_seq / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_restr / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_admin.last_update / _em_software.category ..._em_admin.last_update / _em_software.category / _em_software.fitting_id / _em_software.image_processing_id / _em_software.imaging_id / _em_software.name / _em_software.version / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_scientific_name / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_asym_id / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_asym_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_asym_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_asym_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_asym_id_1 / _ndb_struct_na_base_pair_step.i_auth_asym_id_2 / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.i_label_asym_id_1 / _ndb_struct_na_base_pair_step.i_label_asym_id_2 / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_asym_id_1 / _ndb_struct_na_base_pair_step.j_auth_asym_id_2 / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_asym_id_1 / _ndb_struct_na_base_pair_step.j_label_asym_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_1 / _ndb_struct_na_base_pair_step.j_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 2, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 2.2Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: DNA (28-MER)
P: Maltose/maltodextrin-binding periplasmic protein,Guillardia theta Fanzor1
T: DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*TP*AP*AP*AP*GP*GP*CP*CP*CP*CP*GP*GP*G)-3')
W: RNA (142-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,5555
Polymers224,4904
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (28-MER)


Mass: 24883.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Maltose/maltodextrin-binding periplasmic protein,Guillardia theta Fanzor1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 124818.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Guillardia theta (eukaryote)
Gene: malE, b4034, JW3994, GUITHDRAFT_101477 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0AEX9, UniProt: L1JXG4
#3: DNA chain DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*TP*AP*AP*AP*GP*GP*CP*CP*CP*CP*GP*GP*G)-3')


Mass: 25071.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain RNA (142-MER)


Mass: 49715.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta (eukaryote) / Production host: Saccharomyces cerevisiae (brewer's yeast)
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Guillardia theta Fanzor1-omegaRNA-target DNA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Guillardia theta (eukaryote)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 58.18 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328609 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00188412
ELECTRON MICROSCOPYf_angle_d0.471511943
ELECTRON MICROSCOPYf_chiral_restr0.03491344
ELECTRON MICROSCOPYf_plane_restr0.00291010
ELECTRON MICROSCOPYf_dihedral_angle_d18.3563817

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