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- PDB-8ikp: Cryo-EM structure of hnRAC1-8I fibril -

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Basic information

Entry
Database: PDB / ID: 8ikp
TitleCryo-EM structure of hnRAC1-8I fibril
ComponentsGLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
KeywordsPROTEIN FIBRIL / irreversible peptide fibril
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLi, D.N. / Ma, Y.Y. / Li, D. / Dai, B. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of hnRAC1-8I fibril
Authors: Li, D.N. / Ma, Y.Y. / Li, D. / Dai, B. / Liu, C.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
c: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
A: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
B: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
C: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
D: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
E: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
F: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
G: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
a: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
I: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
L: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
O: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
R: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
U: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
X: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
H: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
b: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
J: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
M: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
P: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
S: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
V: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
Y: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
e: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
d: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
K: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
N: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
Q: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
T: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
W: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
Z: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY
f: GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY


Theoretical massNumber of molelcules
Total (without water)32,31232
Polymers32,31232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
GLY-PHE-GLY-GLY-ASN-ASP-ASN-PHI-GLY


Mass: 1009.760 Da / Num. of mol.: 32 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY

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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: Cryo-EM structure of hnRAC1-8I fibril / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.06 ° / Axial rise/subunit: 4.82 Å / Axial symmetry: C1
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10265 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0062080
ELECTRON MICROSCOPYf_angle_d1.5052752
ELECTRON MICROSCOPYf_dihedral_angle_d11.811896
ELECTRON MICROSCOPYf_chiral_restr0.052160
ELECTRON MICROSCOPYf_plane_restr0.003448

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