+Open data
-Basic information
Entry | Database: PDB / ID: 6mk1 | ||||||
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Title | Cryo-EM of self-assembly peptide filament HEAT_R1 | ||||||
Components | peptide HEAT_R1 | ||||||
Keywords | PROTEIN FIBRIL / filament / self-assembly peptide filament | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6 Å | ||||||
Authors | Wang, F. / Hughes, S.A. / Orlova, A. / Conticello, V.P. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Authors: Spencer A Hughes / Fengbin Wang / Shengyuan Wang / Mark A B Kreutzberger / Tomasz Osinski / Albina Orlova / Joseph S Wall / Xiaobing Zuo / Edward H Egelman / Vincent P Conticello / Abstract: Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 ...Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6mk1.cif.gz | 505.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mk1.ent.gz | 421.5 KB | Display | PDB format |
PDBx/mmJSON format | 6mk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mk1_validation.pdf.gz | 984.4 KB | Display | wwPDB validaton report |
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Full document | 6mk1_full_validation.pdf.gz | 983.8 KB | Display | |
Data in XML | 6mk1_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 6mk1_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/6mk1 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/6mk1 | HTTPS FTP |
-Related structure data
Related structure data | 9136MC 0252C 6hqeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 26 / Rise per n subunits: 3.02 Å / Rotation per n subunits: 34.8 °) |
Details | Apply helical parameters to pairs of chains (e.g., A and a) to build helical assembly. |
-Components
#1: Protein/peptide | Mass: 3374.886 Da / Num. of mol.: 52 / Source method: obtained synthetically Source: (synth.) Methanothermobacter thermautotrophicus (archaea) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: self-assembled peptide filament / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Methanothermobacter thermautotrophicus (archaea) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 7 |
-Processing
Software | Name: PHENIX / Version: dev_2439: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 34.8 ° / Axial rise/subunit: 3.02 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6 Å / Resolution method: OTHER / Num. of particles: 56421 / Algorithm: BACK PROJECTION / Details: Model: Map FSC 0.38 cut off, d99 and d model / Symmetry type: HELICAL | ||||||||||||||||||||||||
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