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- PDB-6mk1: Cryo-EM of self-assembly peptide filament HEAT_R1 -

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Basic information

Entry
Database: PDB / ID: 6mk1
TitleCryo-EM of self-assembly peptide filament HEAT_R1
Componentspeptide HEAT_R1
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6 Å
AuthorsWang, F. / Hughes, S.A. / Orlova, A. / Conticello, V.P. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: 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
DepositionSep 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: peptide HEAT_R1
a: peptide HEAT_R1
B: peptide HEAT_R1
b: peptide HEAT_R1
C: peptide HEAT_R1
c: peptide HEAT_R1
D: peptide HEAT_R1
d: peptide HEAT_R1
E: peptide HEAT_R1
e: peptide HEAT_R1
F: peptide HEAT_R1
f: peptide HEAT_R1
G: peptide HEAT_R1
g: peptide HEAT_R1
H: peptide HEAT_R1
h: peptide HEAT_R1
I: peptide HEAT_R1
i: peptide HEAT_R1
J: peptide HEAT_R1
j: peptide HEAT_R1
K: peptide HEAT_R1
k: peptide HEAT_R1
L: peptide HEAT_R1
l: peptide HEAT_R1
M: peptide HEAT_R1
m: peptide HEAT_R1
N: peptide HEAT_R1
n: peptide HEAT_R1
O: peptide HEAT_R1
o: peptide HEAT_R1
P: peptide HEAT_R1
p: peptide HEAT_R1
Q: peptide HEAT_R1
q: peptide HEAT_R1
R: peptide HEAT_R1
r: peptide HEAT_R1
S: peptide HEAT_R1
s: peptide HEAT_R1
T: peptide HEAT_R1
t: peptide HEAT_R1
U: peptide HEAT_R1
u: peptide HEAT_R1
V: peptide HEAT_R1
v: peptide HEAT_R1
W: peptide HEAT_R1
w: peptide HEAT_R1
X: peptide HEAT_R1
x: peptide HEAT_R1
Y: peptide HEAT_R1
y: peptide HEAT_R1
Z: peptide HEAT_R1
z: peptide HEAT_R1


Theoretical massNumber of molelcules
Total (without water)175,49452
Polymers175,49452
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area63840 Å2
ΔGint-344 kcal/mol
Surface area67740 Å2
SymmetryHelical 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 °)
DetailsApply helical parameters to pairs of chains (e.g., A and a) to build helical assembly.

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Components

#1: Protein/peptide ...
peptide HEAT_R1


Mass: 3374.886 Da / Num. of mol.: 52 / Source method: obtained synthetically
Source: (synth.) Methanothermobacter thermautotrophicus (archaea)

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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: self-assembled peptide filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Methanothermobacter thermautotrophicus (archaea)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: dev_2439: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8PHENIXmodel fitting
10Cootmodel refinement
11PHENIXmodel refinement
15SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 34.8 ° / Axial rise/subunit: 3.02 Å / Axial symmetry: C1
3D reconstructionResolution: 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
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0131040
ELECTRON MICROSCOPYf_angle_d1.33356448
ELECTRON MICROSCOPYf_dihedral_angle_d7.73815872
ELECTRON MICROSCOPYf_chiral_restr0.0482304
ELECTRON MICROSCOPYf_plane_restr0.0084416

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