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- PDB-8gi2: Cryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA2 -

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Entry
Database: PDB / ID: 8gi2
TitleCryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA2
ComponentsNatrinema pilin, PilA2
KeywordsPROTEIN FIBRIL / Helical / Pili / Natrinema / MOTOR PROTEIN
Biological speciesNatrinema sp. J7-2 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsSonani, R.R. / Kreutzberger, M.A.B. / Liu, Y. / Krupovic, M. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
Citation
Journal: Cell Rep / Year: 2025
Title: A type IV pili-mediated mutualism between two co-resident temperate archaeal viruses and their host.
Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H ...Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H Egelman / Shishen Du / Xiangdong Chen /
Abstract: Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea ...Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea remains largely unexplored. Here, we discover a tripartite mutualistic interaction among the co-existing temperate viruses SNJ1 and SNJ2 and their host, haloarchaeon Natrinema sp. J7. We find that the SNJ2 provirus encodes two type IV pilins (T4Ps), which hijack the host secretion machinery to assemble into distinct filaments on the host cell surface. The SNJ2-encoded pili are dispensable for the SNJ2 infection but serve as receptors for SNJ1. As a quid pro quo, SNJ1 enhances the replication of SNJ2. Furthermore, the viral pili are the dominant filaments on the cell surface and promote biofilm formation and motility of the host. A number of SNJ2-like proviruses harbor T4P genes, suggesting that T4P-mediated virus-virus and virus-host interactions are widespread in Haloarchaea.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: The evolution of archaeal flagellar filaments.
Authors: Mark A B Kreutzberger / Virginija Cvirkaite-Krupovic / Ying Liu / Diana P Baquero / Junfeng Liu / Ravi R Sonani / Chris R Calladine / Fengbin Wang / Mart Krupovic / Edward H Egelman /
Abstract: Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
History
DepositionMar 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 16, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jun 18, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_imaging / em_software / entity / pdbx_contact_author / pdbx_entry_details / pdbx_helical_symmetry / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine_ls_restr / struct / struct_conf / struct_keywords / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _em_admin.last_update / _em_imaging.microscope_model / _entity.pdbx_description / _pdbx_helical_symmetry.number_of_operations / _pdbx_helical_symmetry.rise_per_n_subunits / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct.title / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.pdbx_keywords / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atomic clashes
Details: Previous model has higher clash score (~15). The new model has improved clash score (~5).
Provider: author / Type: Coordinate replacement
Revision 1.1Jun 18, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Group: Data collection / Data processing ...Data collection / Data processing / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Category: em_admin / em_imaging ...em_admin / em_imaging / em_software / entity / struct_keywords
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _em_imaging.microscope_model ..._em_admin.last_update / _em_imaging.microscope_model / _entity.pdbx_description / _struct_keywords.pdbx_keywords
Revision 2.1Nov 26, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / struct_keywords
Item: _em_admin.last_update / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natrinema pilin, PilA2


Theoretical massNumber of molelcules
Total (without water)17,0101
Polymers17,0101
Non-polymers00
Water00
1
A: Natrinema pilin, PilA2
x 35


Theoretical massNumber of molelcules
Total (without water)595,34535
Polymers595,34535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation34
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 4.95 Å / Rotation per n subunits: 108.72 °)

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Components

#1: Protein Natrinema pilin, PilA2


Mass: 17009.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Natrinema sp. J7-2 (archaea)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Type IV pili / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 108.72 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261069 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0031048
ELECTRON MICROSCOPYf_angle_d0.6171429
ELECTRON MICROSCOPYf_dihedral_angle_d5.933151
ELECTRON MICROSCOPYf_chiral_restr0.048183
ELECTRON MICROSCOPYf_plane_restr0.002188

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