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- PDB-9nck: Nanotube of computationally designed peptide assembly R3K (16 pro... -

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Basic information

Entry
Database: PDB / ID: 9nck
TitleNanotube of computationally designed peptide assembly R3K (16 protofilament)
ComponentsBundlemer nanotube
KeywordsPROTEIN FIBRIL / Computationally designed peptide / bundlemer / synthetic peptide nanotube
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsDas, A. / Conticello, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nanotube of computationally designed peptide assembly R3K (16 protofilament)
Authors: Das, A. / Conticello, V.
History
DepositionFeb 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bundlemer nanotube
U: Bundlemer nanotube
V: Bundlemer nanotube
W: Bundlemer nanotube
X: Bundlemer nanotube
Y: Bundlemer nanotube
Z: Bundlemer nanotube
a: Bundlemer nanotube
B: Bundlemer nanotube
b: Bundlemer nanotube
c: Bundlemer nanotube
d: Bundlemer nanotube
e: Bundlemer nanotube
f: Bundlemer nanotube
g: Bundlemer nanotube
h: Bundlemer nanotube
C: Bundlemer nanotube
i: Bundlemer nanotube
j: Bundlemer nanotube
k: Bundlemer nanotube
l: Bundlemer nanotube
m: Bundlemer nanotube
n: Bundlemer nanotube
o: Bundlemer nanotube
D: Bundlemer nanotube
p: Bundlemer nanotube
q: Bundlemer nanotube
r: Bundlemer nanotube
s: Bundlemer nanotube
t: Bundlemer nanotube
u: Bundlemer nanotube
v: Bundlemer nanotube
E: Bundlemer nanotube
w: Bundlemer nanotube
x: Bundlemer nanotube
y: Bundlemer nanotube
z: Bundlemer nanotube
0: Bundlemer nanotube
1: Bundlemer nanotube
2: Bundlemer nanotube
F: Bundlemer nanotube
3: Bundlemer nanotube
4: Bundlemer nanotube
5: Bundlemer nanotube
6: Bundlemer nanotube
7: Bundlemer nanotube
8: Bundlemer nanotube
9: Bundlemer nanotube
G: Bundlemer nanotube
AA: Bundlemer nanotube
BA: Bundlemer nanotube
CA: Bundlemer nanotube
DA: Bundlemer nanotube
EA: Bundlemer nanotube
FA: Bundlemer nanotube
GA: Bundlemer nanotube
H: Bundlemer nanotube
HA: Bundlemer nanotube
IA: Bundlemer nanotube
JA: Bundlemer nanotube
KA: Bundlemer nanotube
LA: Bundlemer nanotube
MA: Bundlemer nanotube
NA: Bundlemer nanotube
I: Bundlemer nanotube
OA: Bundlemer nanotube
PA: Bundlemer nanotube
QA: Bundlemer nanotube
RA: Bundlemer nanotube
SA: Bundlemer nanotube
TA: Bundlemer nanotube
UA: Bundlemer nanotube
J: Bundlemer nanotube
VA: Bundlemer nanotube
WA: Bundlemer nanotube
XA: Bundlemer nanotube
YA: Bundlemer nanotube
ZA: Bundlemer nanotube
aA: Bundlemer nanotube
bA: Bundlemer nanotube
K: Bundlemer nanotube
cA: Bundlemer nanotube
dA: Bundlemer nanotube
eA: Bundlemer nanotube
fA: Bundlemer nanotube
gA: Bundlemer nanotube
hA: Bundlemer nanotube
iA: Bundlemer nanotube
L: Bundlemer nanotube
jA: Bundlemer nanotube
kA: Bundlemer nanotube
lA: Bundlemer nanotube
mA: Bundlemer nanotube
nA: Bundlemer nanotube
oA: Bundlemer nanotube
pA: Bundlemer nanotube
M: Bundlemer nanotube
qA: Bundlemer nanotube
rA: Bundlemer nanotube
sA: Bundlemer nanotube
tA: Bundlemer nanotube
uA: Bundlemer nanotube
vA: Bundlemer nanotube
wA: Bundlemer nanotube
N: Bundlemer nanotube
xA: Bundlemer nanotube
yA: Bundlemer nanotube
zA: Bundlemer nanotube
0A: Bundlemer nanotube
1A: Bundlemer nanotube
2A: Bundlemer nanotube
3A: Bundlemer nanotube
O: Bundlemer nanotube
4A: Bundlemer nanotube
5A: Bundlemer nanotube
6A: Bundlemer nanotube
7A: Bundlemer nanotube
8A: Bundlemer nanotube
9A: Bundlemer nanotube
AB: Bundlemer nanotube
P: Bundlemer nanotube
BB: Bundlemer nanotube
CB: Bundlemer nanotube
DB: Bundlemer nanotube
EB: Bundlemer nanotube
FB: Bundlemer nanotube
GB: Bundlemer nanotube
HB: Bundlemer nanotube
Q: Bundlemer nanotube
IB: Bundlemer nanotube
JB: Bundlemer nanotube
KB: Bundlemer nanotube
LB: Bundlemer nanotube
MB: Bundlemer nanotube
NB: Bundlemer nanotube
OB: Bundlemer nanotube
R: Bundlemer nanotube
PB: Bundlemer nanotube
QB: Bundlemer nanotube
RB: Bundlemer nanotube
SB: Bundlemer nanotube
TB: Bundlemer nanotube
UB: Bundlemer nanotube
VB: Bundlemer nanotube
S: Bundlemer nanotube
WB: Bundlemer nanotube
XB: Bundlemer nanotube
YB: Bundlemer nanotube
ZB: Bundlemer nanotube
aB: Bundlemer nanotube
bB: Bundlemer nanotube
cB: Bundlemer nanotube
T: Bundlemer nanotube
dB: Bundlemer nanotube
eB: Bundlemer nanotube
fB: Bundlemer nanotube
gB: Bundlemer nanotube
hB: Bundlemer nanotube
iB: Bundlemer nanotube
jB: Bundlemer nanotube


Theoretical massNumber of molelcules
Total (without water)502,824160
Polymers502,824160
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Bundlemer nanotube


Mass: 3142.652 Da / Num. of mol.: 160 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN
Has protein modificationY

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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: Nanotube of computationally designed peptide assembly R3K (16 protofilament)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 4.5
Buffer componentConc.: 10 mM / Name: Acetate / Formula: C2H3NaO2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 296 K

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7ISOLDEmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 22.83 ° / Axial rise/subunit: 4.155 Å / Axial symmetry: C1
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44140 / Symmetry type: HELICAL
Atomic model buildingB value: 92.4 / Space: REAL
RefinementHighest resolution: 3.58 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01135200
ELECTRON MICROSCOPYf_angle_d1.46746720
ELECTRON MICROSCOPYf_dihedral_angle_d12.67513120
ELECTRON MICROSCOPYf_chiral_restr0.0684640
ELECTRON MICROSCOPYf_plane_restr0.0126080

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