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- PDB-6wl8: Cryo-EM of Form 2 peptide filament -

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Basic information

Entry
Database: PDB / ID: 6wl8
TitleCryo-EM of Form 2 peptide filament
ComponentsForm 2 peptide
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang, F. / Gnewou, O.M. / Xu, C. / Su, Z. / Egelman, E.H. / Conticello, V.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials.
Authors: Fengbin Wang / Ordy Gnewou / Charles Modlin / Leticia C Beltran / Chunfu Xu / Zhangli Su / Puneet Juneja / Gevorg Grigoryan / Edward H Egelman / Vincent P Conticello /
Abstract: The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of ...The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 2, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Form 2 peptide
0: Form 2 peptide
B: Form 2 peptide
2: Form 2 peptide
C: Form 2 peptide
3: Form 2 peptide
D: Form 2 peptide
4: Form 2 peptide
E: Form 2 peptide
5: Form 2 peptide
F: Form 2 peptide
6: Form 2 peptide
G: Form 2 peptide
7: Form 2 peptide
H: Form 2 peptide
8: Form 2 peptide
I: Form 2 peptide
9: Form 2 peptide
J: Form 2 peptide
AA: Form 2 peptide
K: Form 2 peptide
BA: Form 2 peptide
L: Form 2 peptide
CA: Form 2 peptide
M: Form 2 peptide
DA: Form 2 peptide
N: Form 2 peptide
EA: Form 2 peptide
O: Form 2 peptide
FA: Form 2 peptide
P: Form 2 peptide
GA: Form 2 peptide
Q: Form 2 peptide
HA: Form 2 peptide
R: Form 2 peptide
IA: Form 2 peptide
S: Form 2 peptide
JA: Form 2 peptide
T: Form 2 peptide
KA: Form 2 peptide
U: Form 2 peptide
LA: Form 2 peptide
V: Form 2 peptide
MA: Form 2 peptide
W: Form 2 peptide
NA: Form 2 peptide
X: Form 2 peptide
OA: Form 2 peptide
Y: Form 2 peptide
PA: Form 2 peptide
Z: Form 2 peptide
QA: Form 2 peptide
a: Form 2 peptide
RA: Form 2 peptide
b: Form 2 peptide
SA: Form 2 peptide
c: Form 2 peptide
TA: Form 2 peptide
d: Form 2 peptide
UA: Form 2 peptide
e: Form 2 peptide
VA: Form 2 peptide
f: Form 2 peptide
WA: Form 2 peptide
g: Form 2 peptide
XA: Form 2 peptide
h: Form 2 peptide
YA: Form 2 peptide
i: Form 2 peptide
ZA: Form 2 peptide
j: Form 2 peptide
aA: Form 2 peptide
k: Form 2 peptide
bA: Form 2 peptide
l: Form 2 peptide
cA: Form 2 peptide
m: Form 2 peptide
dA: Form 2 peptide
n: Form 2 peptide
eA: Form 2 peptide
o: Form 2 peptide
fA: Form 2 peptide
p: Form 2 peptide
gA: Form 2 peptide
q: Form 2 peptide
hA: Form 2 peptide
r: Form 2 peptide
iA: Form 2 peptide
s: Form 2 peptide
jA: Form 2 peptide
t: Form 2 peptide
kA: Form 2 peptide
u: Form 2 peptide
lA: Form 2 peptide
v: Form 2 peptide
mA: Form 2 peptide
w: Form 2 peptide
nA: Form 2 peptide
x: Form 2 peptide
oA: Form 2 peptide
y: Form 2 peptide
pA: Form 2 peptide
z: Form 2 peptide
qA: Form 2 peptide
1: Form 2 peptide
rA: Form 2 peptide


Theoretical massNumber of molelcules
Total (without water)338,961106
Polymers338,961106
Non-polymers00
Water00
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 area185340 Å2
ΔGint-1851 kcal/mol
Surface area134320 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 106 / Rise per n subunits: 1.93 Å / Rotation per n subunits: 124.36 °)

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Components

#1: Protein/peptide ...
Form 2 peptide


Mass: 3197.741 Da / Num. of mol.: 106 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: self-assembly Form 2 peptide filament / Type: COMPLEX / Details: synthetic peptide / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 124.36 ° / Axial rise/subunit: 1.93 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 408751 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL

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