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- PDB-9ncj: Coiled-coil bundlemer nanotube, R3K (15 proto-filaments) -

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Basic information

Entry
Database: PDB / ID: 9ncj
TitleCoiled-coil bundlemer nanotube, R3K (15 proto-filaments)
ComponentsR3K nanotube
KeywordsPROTEIN FIBRIL / Synthetic Construct / Nanotube / Bundlemer / coiled-coil
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.93 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: Coiled-coil bundlemer nanotube, R3K (15 proto-filaments)
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: R3K nanotube
S: R3K nanotube
T: R3K nanotube
U: R3K nanotube
V: R3K nanotube
W: R3K nanotube
X: R3K nanotube
Y: R3K nanotube
B: R3K nanotube
Z: R3K nanotube
a: R3K nanotube
b: R3K nanotube
c: R3K nanotube
d: R3K nanotube
e: R3K nanotube
f: R3K nanotube
C: R3K nanotube
g: R3K nanotube
h: R3K nanotube
i: R3K nanotube
j: R3K nanotube
k: R3K nanotube
l: R3K nanotube
m: R3K nanotube
D: R3K nanotube
n: R3K nanotube
o: R3K nanotube
p: R3K nanotube
q: R3K nanotube
r: R3K nanotube
s: R3K nanotube
t: R3K nanotube
E: R3K nanotube
u: R3K nanotube
v: R3K nanotube
w: R3K nanotube
x: R3K nanotube
y: R3K nanotube
z: R3K nanotube
0: R3K nanotube
F: R3K nanotube
1: R3K nanotube
2: R3K nanotube
3: R3K nanotube
4: R3K nanotube
5: R3K nanotube
6: R3K nanotube
7: R3K nanotube
G: R3K nanotube
8: R3K nanotube
9: R3K nanotube
AA: R3K nanotube
BA: R3K nanotube
CA: R3K nanotube
DA: R3K nanotube
EA: R3K nanotube
H: R3K nanotube
FA: R3K nanotube
GA: R3K nanotube
HA: R3K nanotube
IA: R3K nanotube
JA: R3K nanotube
KA: R3K nanotube
LA: R3K nanotube
I: R3K nanotube
MA: R3K nanotube
NA: R3K nanotube
OA: R3K nanotube
PA: R3K nanotube
QA: R3K nanotube
RA: R3K nanotube
SA: R3K nanotube
J: R3K nanotube
TA: R3K nanotube
UA: R3K nanotube
VA: R3K nanotube
WA: R3K nanotube
XA: R3K nanotube
YA: R3K nanotube
ZA: R3K nanotube
K: R3K nanotube
aA: R3K nanotube
bA: R3K nanotube
cA: R3K nanotube
dA: R3K nanotube
eA: R3K nanotube
fA: R3K nanotube
gA: R3K nanotube
L: R3K nanotube
hA: R3K nanotube
iA: R3K nanotube
jA: R3K nanotube
kA: R3K nanotube
lA: R3K nanotube
mA: R3K nanotube
nA: R3K nanotube
M: R3K nanotube
oA: R3K nanotube
pA: R3K nanotube
qA: R3K nanotube
rA: R3K nanotube
sA: R3K nanotube
tA: R3K nanotube
uA: R3K nanotube
N: R3K nanotube
vA: R3K nanotube
wA: R3K nanotube
xA: R3K nanotube
yA: R3K nanotube
zA: R3K nanotube
0A: R3K nanotube
1A: R3K nanotube
O: R3K nanotube
2A: R3K nanotube
3A: R3K nanotube
4A: R3K nanotube
5A: R3K nanotube
6A: R3K nanotube
7A: R3K nanotube
8A: R3K nanotube
P: R3K nanotube
9A: R3K nanotube
AB: R3K nanotube
BB: R3K nanotube
CB: R3K nanotube
DB: R3K nanotube
EB: R3K nanotube
FB: R3K nanotube
Q: R3K nanotube
GB: R3K nanotube
HB: R3K nanotube
IB: R3K nanotube
JB: R3K nanotube
KB: R3K nanotube
LB: R3K nanotube
MB: R3K nanotube
R: R3K nanotube
NB: R3K nanotube
OB: R3K nanotube
PB: R3K nanotube
QB: R3K nanotube
RB: R3K nanotube
SB: R3K nanotube
TB: R3K nanotube


Theoretical massNumber of molelcules
Total (without water)452,542144
Polymers452,542144
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 ...
R3K nanotube


Mass: 3142.652 Da / Num. of mol.: 144 / 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: Coiled-coil bundlemer nanotube, R3K (15 proto-filaments)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 4.5
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: 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
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 24.347 ° / Axial rise/subunit: 4.441 Å / Axial symmetry: C1
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66965 / Symmetry type: HELICAL
Atomic model buildingB value: 105.5
RefinementHighest resolution: 3.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01431680
ELECTRON MICROSCOPYf_angle_d1.43542048
ELECTRON MICROSCOPYf_dihedral_angle_d12.4111808
ELECTRON MICROSCOPYf_chiral_restr0.0784176
ELECTRON MICROSCOPYf_plane_restr0.0135472

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