[English] 日本語
Yorodumi
- PDB-7sxn: Orb2A residues 1-9 MYNKFVNFI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sxn
TitleOrb2A residues 1-9 MYNKFVNFI
ComponentsOrb2A residues 1-9 MYNKFVNFI
KeywordsPROTEIN FIBRIL / amyloid / long-term memory / micro-ED / Orb2A
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.05 Å
AuthorsBowler, J.T. / Sawaya, M.R. / Boyer, D.R. / Cascio, D. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1616265 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Micro-electron diffraction structure of the aggregation-driving N terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets.
Authors: Jeannette T Bowler / Michael R Sawaya / David R Boyer / Duilio Cascio / Manya Bali / David S Eisenberg /
Abstract: Amyloid protein aggregation is commonly associated with progressive neurodegenerative diseases, however not all amyloid fibrils are pathogenic. The neuronal cytoplasmic polyadenylation element ...Amyloid protein aggregation is commonly associated with progressive neurodegenerative diseases, however not all amyloid fibrils are pathogenic. The neuronal cytoplasmic polyadenylation element binding protein is a regulator of synaptic mRNA translation and has been shown to form functional amyloid aggregates that stabilize long-term memory. In adult Drosophila neurons, the cytoplasmic polyadenylation element binding homolog Orb2 is expressed as 2 isoforms, of which the Orb2B isoform is far more abundant, but the rarer Orb2A isoform is required to initiate Orb2 aggregation. The N terminus is a distinctive feature of the Orb2A isoform and is critical for its aggregation. Intriguingly, replacement of phenylalanine in the fifth position of Orb2A with tyrosine (F5Y) in Drosophila impairs stabilization of long-term memory. The structure of endogenous Orb2B fibers was recently determined by cryo-EM, but the structure adopted by fibrillar Orb2A is less certain. Here we use micro-electron diffraction to determine the structure of the first 9 N-terminal residues of Orb2A, at a resolution of 1.05 Å. We find that this segment (which we term M9I) forms an amyloid-like array of parallel in-register β-sheets, which interact through side chain interdigitation of aromatic and hydrophobic residues. Our structure provides an explanation for the decreased aggregation observed for the F5Y mutant and offers a hypothesis for how the addition of a single atom (the tyrosyl oxygen) affects long-term memory. We also propose a structural model of Orb2A that integrates our structure of the M9I segment with the published Orb2B cryo-EM structure.
History
DepositionNov 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 14, 2023Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Orb2A residues 1-9 MYNKFVNFI


Theoretical massNumber of molelcules
Total (without water)1,1761
Polymers1,1761
Non-polymers00
Water724
1
AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI

AAA: Orb2A residues 1-9 MYNKFVNFI


  • defined by author
  • Evidence: electron microscopy
  • 11.8 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)11,76410
Polymers11,76410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
crystal symmetry operation2_746-x+2,y-1/2,-z+11
crystal symmetry operation2_846-x+3,y-1/2,-z+11
crystal symmetry operation2_946-x+4,y-1/2,-z+11
Unit cell
Length a, b, c (Å)4.830, 23.100, 29.840
Angle α, β, γ (deg.)90.000, 92.001, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide Orb2A residues 1-9 MYNKFVNFI


Mass: 1176.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Amyloid fibril of Orb2A residues 1-9 MYNKFVNFI / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 4.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Data collection

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: DIFFRACTION
Image recordingElectron dose: 0.01 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffractionCamera length: 1344 mm
EM diffraction shellResolution: 1.05→1.08 Å / Fourier space coverage: 69.9 % / Multiplicity: 7.2 / Num. of structure factors: 1101 / Phase residual: 0.1 °
EM diffraction statsFourier space coverage: 83.3 % / High resolution: 1.05 Å / Num. of intensities measured: 36014 / Num. of structure factors: 2596 / Phase error rejection criteria: 0.1 / Rmerge: 15.6
Diffraction sourceSource: ELECTRON MICROSCOPE / Wavelength: 0.0251 Å
DetectorDate: Oct 17, 2018
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1.05→18.262 Å / Num. obs: 2596 / % possible obs: 83.3 % / Redundancy: 13.873 % / Biso Wilson estimate: 12.406 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.161 / Χ2: 0.835 / Net I/σ(I): 8.24 / Num. measured all: 36014 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.087.1960.7121.7911012191530.5720.77669.9
1.08-1.118.0640.592.2912662191570.7850.63271.7
1.11-1.1411.5140.4733.6820842271810.9020.49379.7
1.14-1.1714.4160.4394.6926672271850.8240.45681.5
1.17-1.2115.4640.4235.1330312211960.8630.43888.7
1.21-1.2613.110.4314.7320191801540.8560.44985.6
1.26-1.312.8140.3625.2719991811560.950.37986.2
1.3-1.3613.7210.3436.0820171691470.9720.35787
1.36-1.4215.4710.3326.8823671731530.9190.34388.4
1.42-1.4817.5610.3138.7727571791570.8920.32387.7
1.48-1.5718.5160.2111.5829811811610.9830.21689
1.57-1.6616.180.19511.9621521561330.9580.20285.3
1.66-1.7712.4590.21110.8713831311110.9790.22184.7
1.77-1.9212.990.19612.4913121171010.9690.20586.3
1.92-2.114.6610.17214.9816861331150.9850.17986.5
2.1-2.3518.5190.16217.6420001251080.9710.16886.4
2.35-2.7114.2570.14816.1105593740.9920.15379.6
2.71-3.3212.5970.1215.7478176620.9860.12581.6
3.32-4.715.8610.09718.66114280720.9910.10190
4.7-18.26210.70.14714.4821431200.9930.15164.5

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 92 ° / ∠γ: 90 ° / A: 4.83 Å / B: 23.1 Å / C: 29.8 Å / Space group name: P21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingSpace: RECIPROCAL
RefinementResolution: 1.05→18.262 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.226 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.045
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.201 260 10.015 %
Rwork0.1809 2336 -
all0.183 --
obs-2596 83.258 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.579 Å2-0 Å20.131 Å2
2---0.41 Å20 Å2
3----0.178 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0150.01285
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0030.01882
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.8431.654113
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.6381.603185
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.54458
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg47.531245
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg15.0621515
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.1080.210
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0110.0298
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0020.0226
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.1380.28
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.1910.252
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.1940.239
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0790.244
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.2540.21
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.0510.25
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.2340.219
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.3560.21
ELECTRON CRYSTALLOGRAPHYr_mcbond_it2.5430.7735
ELECTRON CRYSTALLOGRAPHYr_mcbond_other2.1040.73434
ELECTRON CRYSTALLOGRAPHYr_mcangle_it2.3461.16140
ELECTRON CRYSTALLOGRAPHYr_mcangle_other2.3451.17141
ELECTRON CRYSTALLOGRAPHYr_scbond_it3.0360.99650
ELECTRON CRYSTALLOGRAPHYr_scbond_other3.0370.97950
ELECTRON CRYSTALLOGRAPHYr_scangle_it2.5361.37170
ELECTRON CRYSTALLOGRAPHYr_scangle_other2.5181.37371
ELECTRON CRYSTALLOGRAPHYr_lrange_it3.3038.66182
ELECTRON CRYSTALLOGRAPHYr_lrange_other3.2988.76583
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr9.4693167
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.05-1.1730.303670.2336070.248900.8820.90875.73030.192
1.173-1.3540.24660.25870.2047500.8750.91187.06670.175
1.354-1.6560.243600.1785410.1856860.9140.93987.60930.171
1.656-2.3320.214430.193930.1925080.9420.94285.82680.214
2.332-18.2620.133240.1472080.1452830.9790.97481.97880.172

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more