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- PDB-6wkx: Cryo-EM of Form 1 related peptide filament, 15-10-3 -

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Basic information

Entry
Database: PDB / ID: 6wkx
TitleCryo-EM of Form 1 related peptide filament, 15-10-3
Componentspeptide 15-10-3
KeywordsPROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, F. / Gnewou, O.M. / 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 17, 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 1.3May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 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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Assembly

Deposited unit
A: peptide 15-10-3
V: peptide 15-10-3
W: peptide 15-10-3
X: peptide 15-10-3
Y: peptide 15-10-3
B: peptide 15-10-3
Z: peptide 15-10-3
a: peptide 15-10-3
b: peptide 15-10-3
c: peptide 15-10-3
C: peptide 15-10-3
d: peptide 15-10-3
e: peptide 15-10-3
f: peptide 15-10-3
g: peptide 15-10-3
D: peptide 15-10-3
h: peptide 15-10-3
i: peptide 15-10-3
j: peptide 15-10-3
k: peptide 15-10-3
E: peptide 15-10-3
l: peptide 15-10-3
m: peptide 15-10-3
n: peptide 15-10-3
o: peptide 15-10-3
F: peptide 15-10-3
p: peptide 15-10-3
q: peptide 15-10-3
r: peptide 15-10-3
s: peptide 15-10-3
G: peptide 15-10-3
t: peptide 15-10-3
u: peptide 15-10-3
v: peptide 15-10-3
w: peptide 15-10-3
H: peptide 15-10-3
x: peptide 15-10-3
y: peptide 15-10-3
z: peptide 15-10-3
0: peptide 15-10-3
I: peptide 15-10-3
1: peptide 15-10-3
2: peptide 15-10-3
3: peptide 15-10-3
4: peptide 15-10-3
J: peptide 15-10-3
5: peptide 15-10-3
6: peptide 15-10-3
7: peptide 15-10-3
8: peptide 15-10-3
K: peptide 15-10-3
9: peptide 15-10-3
AA: peptide 15-10-3
BA: peptide 15-10-3
CA: peptide 15-10-3
L: peptide 15-10-3
DA: peptide 15-10-3
EA: peptide 15-10-3
FA: peptide 15-10-3
GA: peptide 15-10-3
M: peptide 15-10-3
HA: peptide 15-10-3
IA: peptide 15-10-3
JA: peptide 15-10-3
KA: peptide 15-10-3
N: peptide 15-10-3
LA: peptide 15-10-3
MA: peptide 15-10-3
NA: peptide 15-10-3
OA: peptide 15-10-3
O: peptide 15-10-3
PA: peptide 15-10-3
QA: peptide 15-10-3
RA: peptide 15-10-3
SA: peptide 15-10-3
P: peptide 15-10-3
TA: peptide 15-10-3
UA: peptide 15-10-3
VA: peptide 15-10-3
WA: peptide 15-10-3
Q: peptide 15-10-3
XA: peptide 15-10-3
YA: peptide 15-10-3
ZA: peptide 15-10-3
aA: peptide 15-10-3
R: peptide 15-10-3
bA: peptide 15-10-3
cA: peptide 15-10-3
dA: peptide 15-10-3
eA: peptide 15-10-3
S: peptide 15-10-3
fA: peptide 15-10-3
gA: peptide 15-10-3
hA: peptide 15-10-3
iA: peptide 15-10-3
T: peptide 15-10-3
jA: peptide 15-10-3
kA: peptide 15-10-3
lA: peptide 15-10-3
mA: peptide 15-10-3
U: peptide 15-10-3
nA: peptide 15-10-3
oA: peptide 15-10-3
pA: peptide 15-10-3
qA: peptide 15-10-3


Theoretical massNumber of molelcules
Total (without water)183,435105
Polymers183,435105
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 area126730 Å2
ΔGint-349 kcal/mol
Surface area51370 Å2
SymmetryHelical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 105 / Rise per n subunits: 9.23 Å / Rotation per n subunits: 9.31 °)

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Components

#1: Protein/peptide ...
peptide 15-10-3


Mass: 1747.004 Da / Num. of mol.: 105 / 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 peptide filament, 15-10-3 / 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
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 9.31 ° / Axial rise/subunit: 9.23 Å / Axial symmetry: C5
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 14700 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612915
ELECTRON MICROSCOPYf_angle_d0.52817325
ELECTRON MICROSCOPYf_dihedral_angle_d20.6828190
ELECTRON MICROSCOPYf_chiral_restr0.0381995
ELECTRON MICROSCOPYf_plane_restr0.0022310

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