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- PDB-6vps: Cryo-EM structure of the amyloid core of Drosophila Orb2 isolated... -

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Basic information

Entry
Database: PDB / ID: 6vps
TitleCryo-EM structure of the amyloid core of Drosophila Orb2 isolated from head
ComponentsTranslational regulator orb2
KeywordsPROTEIN FIBRIL / amyloid / prion-like / long-term memory
Function / homology
Function and homology information


dendrite terminus / : / sperm axoneme assembly / male courtship behavior / asymmetric cell division / sperm individualization / translation activator activity / translation factor activity, RNA binding / male meiosis I / negative regulation of cytoplasmic translation ...dendrite terminus / : / sperm axoneme assembly / male courtship behavior / asymmetric cell division / sperm individualization / translation activator activity / translation factor activity, RNA binding / male meiosis I / negative regulation of cytoplasmic translation / long-term memory / axon terminus / mRNA regulatory element binding translation repressor activity / positive regulation of translation / synaptic membrane / mRNA 3'-UTR binding / ribosome binding / presynapse / cell cortex / cell body / spermatogenesis / perikaryon / postsynapse / negative regulation of translation / protein stabilization / neuron projection / axon / synapse / perinuclear region of cytoplasm / protein-containing complex / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic polyadenylation element-binding protein, ZZ domain / Cytoplasmic polyadenylation element-binding protein / CEBP, ZZ domain superfamily / Cytoplasmic polyadenylation element-binding protein ZZ domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Translational regulator orb2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHervas, R. / Rau, M.J. / Park, Y. / Zhang, W. / Murzin, A.G. / Fitzpatrick, J.A.J. / Scheres, S.H.W. / Si, K.
CitationJournal: Science / Year: 2020
Title: Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in .
Authors: Ruben Hervas / Michael J Rau / Younshim Park / Wenjuan Zhang / Alexey G Murzin / James A J Fitzpatrick / Sjors H W Scheres / Kausik Si /
Abstract: How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a ...How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element-binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo-electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and "seed" for further translationally active aggregation. The 31-amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Translational regulator orb2
B: Translational regulator orb2
C: Translational regulator orb2
D: Translational regulator orb2
E: Translational regulator orb2
F: Translational regulator orb2
G: Translational regulator orb2
H: Translational regulator orb2
I: Translational regulator orb2


Theoretical massNumber of molelcules
Total (without water)35,7689
Polymers35,7689
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Cryo-Electron Microscopy Negative-Stain Electron Microscopy SDD-AGE PAGE SDS-PAGE Antidody reactivity ThT binding Proteinase K resistance
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20530 Å2
ΔGint33 kcal/mol
Surface area13880 Å2
SymmetryHelical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 9 / Rise per n subunits: 4.75 Å / Rotation per n subunits: -1.55 °)

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Components

#1: Protein/peptide
Translational regulator orb2


Mass: 3974.170 Da / Num. of mol.: 9 / Fragment: UNP residues 176-206 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VSR3

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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: amyloid core of Drosophila Orb2 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Drosophila melanogaster (fruit fly) / Tissue: head
Buffer solutionpH: 7.25
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: 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: 63 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0256 / Classification: refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.55 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C3
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19509 / Symmetry type: HELICAL
RefinementResolution: 2.6→86.72 Å / Cor.coef. Fo:Fc: 0.854 / WRfactor Rwork: 0.322 / SU B: 10.458 / SU ML: 0.21 / Average fsc overall: 0.8918 / Average fsc work: 0.8918 / ESU R: 0.37
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3216 24927 -
all0.322 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 46.615 Å2
Baniso -1Baniso -2Baniso -3
1-3.964 Å2-0.057 Å2-0.012 Å2
2--3.926 Å2-0.015 Å2
3----7.89 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.0122865
ELECTRON MICROSCOPYr_angle_refined_deg0.9981.6163861
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.5825324
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.93726.667270
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.63315513
ELECTRON MICROSCOPYr_chiral_restr0.1310.2306
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.022484
ELECTRON MICROSCOPYr_nbd_refined0.1530.21810
ELECTRON MICROSCOPYr_nbtor_refined0.2680.23004
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1060.2206
ELECTRON MICROSCOPYr_mcbond_it5.5233.9521188
ELECTRON MICROSCOPYr_mcangle_it8.5535.8361494
ELECTRON MICROSCOPYr_scbond_it8.5764.8981677
ELECTRON MICROSCOPYr_scangle_it13.6297.0772349
ELECTRON MICROSCOPYr_lrange_it17.63653.9663568
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.6-2.6670.61218170.61218170.7170.612
2.667-2.7410.59317960.59317960.7260.593
2.741-2.820.43918190.43918190.8430.439
2.82-2.9070.40916420.40916420.8730.409
2.907-3.0020.40116020.40116020.8580.401
3.002-3.1070.37516660.37516660.9180.375
3.107-3.2240.27815230.27815230.9340.278
3.224-3.3560.25214460.25214460.9390.252
3.356-3.5050.26214520.26214520.9440.262
3.505-3.6750.24813290.24813290.9580.248
3.675-3.8740.23512680.23512680.960.235
3.874-4.1080.22312560.22312560.960.223
4.108-4.3910.2310990.2310990.9560.23
4.391-4.7420.27911330.27911330.9690.279
4.742-5.1930.2469340.2469340.950.246
5.193-5.8030.2089030.2089030.970.208
5.803-6.6960.4147840.4147840.8930.414
6.696-8.1890.4046450.4046450.8660.404
8.189-11.530.5015190.5015190.8890.501
11.53-86.720.7732940.7732940.9340.773

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