+Open data
-Basic information
Entry | Database: PDB / ID: 6hqe | ||||||
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Title | Cryo-EM of self-assembly peptide filament LRV_M3delta1 | ||||||
Components | peptide LRV_M3delta1 | ||||||
Keywords | PROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Osinski, T. / Wang, F. / Hughes, S.A. / Kreutzberger, M.A.B. / 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 | 6hqe.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hqe.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 6hqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hqe_validation.pdf.gz | 823.7 KB | Display | wwPDB validaton report |
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Full document | 6hqe_full_validation.pdf.gz | 823 KB | Display | |
Data in XML | 6hqe_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 6hqe_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/6hqe ftp://data.pdbj.org/pub/pdb/validation_reports/hq/6hqe | HTTPS FTP |
-Related structure data
Related structure data | 0252MC 9136C 6mk1C 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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-Components
#1: Protein/peptide | Mass: 2579.933 Da / Num. of mol.: 52 / Source method: obtained synthetically / Source: (synth.) Azotobacter vinelandii (bacteria) |
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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-assembly peptide filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Azotobacter vinelandii (bacteria) |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: dev_2919: / 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: -20.7 ° / Axial rise/subunit: 1.15 Å / Axial symmetry: C1 | |||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: OTHER / Num. of particles: 62616 / Algorithm: BACK PROJECTION / Details: Model:Map FSC 0.38 cut off, d99 and d model / Symmetry type: HELICAL |