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- PDB-7n2e: MicroED structure of human CPEB3 segment (154-161) straight polymorph -

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Basic information

Entry
Database: PDB / ID: 7n2e
TitleMicroED structure of human CPEB3 segment (154-161) straight polymorph
ComponentsCPEB3
KeywordsPROTEIN FIBRIL / functional amyloid / MicroED / amyloid
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1 Å
AuthorsFlores, M.D. / Richards, L.S. / Zee, C.T. / Glynn, C. / Gallagher-Jones, M. / Sawaya, M.R.
Funding support United States, Brazil, Spain, 13items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128867 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136614 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI143368 United States
Sao Paulo Research Foundation (FAPESP)16/24191-8 United States
Sao Paulo Research Foundation (FAPESP)17/13485-3 Brazil
Spanish Ministry of Science, Innovation, and UniversitiesBES-2015-071397 United States
Spanish Ministry of Economy and CompetitivenessPGC2018-101370-B-100, Spain
Spanish Ministry of Economy and CompetitivenessMDM2014-0435-01 Spain
Other government2017SGR- 1192 Spain
CitationJournal: ACS Bio Med Chem Au / Year: 2023
Title: Fragment-Based Phasing of Peptidic Nanocrystals by MicroED.
Authors: Logan S Richards / Maria D Flores / Claudia Millán / Calina Glynn / Chih-Te Zee / Michael R Sawaya / Marcus Gallagher-Jones / Rafael J Borges / Isabel Usón / Jose A Rodriguez /
Abstract: Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic ...Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: CPEB3


Theoretical massNumber of molelcules
Total (without water)8581
Polymers8581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.830, 16.290, 29.020
Angle α, β, γ (deg.)90.000, 94.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CPEB3


Mass: 857.951 Da / Num. of mol.: 1 / Fragment: residues 154-161 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Steric zipper structure of huCPEB3 (154-161) / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.858 kDa/nm / Experimental value: YES
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 0.05 e/Å2 / Film or detector model: OTHER
EM diffractionCamera length: 750 mm
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
7.0971-2.13681110210.01
2.1368-1.70382178.45.812070.01
1.7038-1.490731775.31840.01
1.4907-1.355441816.122090.01
1.3554-1.25885180.46.132130.01
1.2588-1.18561795.361990.01
1.185-1.12597178.85.4831860.01
1.1259-1.0778182.56.532210.01
1.077-1.03579180.96.192120.01
1.0357-1.000110181.15.941930.01
EM diffraction statsDetails: Phase error and phase residual statistics are not routinely reported for crystallographic structures. No imaging was used. The phases were obtained by an ab initio crystallographic method ...Details: Phase error and phase residual statistics are not routinely reported for crystallographic structures. No imaging was used. The phases were obtained by an ab initio crystallographic method described in our manuscript
Fourier space coverage: 79.6 % / High resolution: 1 Å / Num. of intensities measured: 11581 / Num. of structure factors: 1976 / Phase error: 33.78 ° / Phase residual: 0.01 ° / Phase error rejection criteria: 0 / Rmerge: 0.1524 / Rsym: 0.154
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1→7.097 Å / Num. obs: 1976 / % possible obs: 79.6 % / Redundancy: 5.861 % / Biso Wilson estimate: 6.41 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.167 / Χ2: 0.946 / Net I/σ(I): 7.24 / Num. measured all: 11581 / Scaling rejects: 8
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
1-1.035.2950.3233.46991631320.9160.35881
1.03-1.055.9630.2144.728111661360.980.23581.9
1.05-1.086.0430.2035.248341751380.9850.22278.9
1.08-1.126.0990.1945.668601751410.980.21280.6
1.12-1.156.6090.17479121681380.9690.18882.1
1.15-1.26.4450.2276.489411811460.960.24780.7
1.2-1.245.1620.1926.116041451170.9680.21480.7
1.24-1.295.1210.1636.615481371070.9740.18278.1
1.29-1.355.730.1547.615731281000.9910.1778.1
1.35-1.415.7040.1926.896161381080.9570.21178.3
1.41-1.496.4460.1737.67221341120.9840.18883.6
1.49-1.586.7740.1749.827791411150.9650.18881.6
1.58-1.695.2640.1439.04458109870.9810.15879.8
1.69-1.834.8240.1438.5332890680.9850.1675.6
1.83-25.3240.1329.6339496740.9910.14577.1
2-2.246.280.12910.9515105820.9880.14378.1
2.24-2.586.5080.15611.4441081630.9850.17177.8
2.58-3.164.8260.10310.0722260460.9990.11376.7
3.16-4.475.2350.11210.7526760510.9740.12885
4.47-7.0975.8670.11611.118829150.9960.12351.7

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.27data extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 94.605 ° / ∠γ: 90 ° / A: 4.83 Å / B: 16.29 Å / C: 29.02 Å / Space group name: P1211 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: AB INITIO MODEL
RefinementResolution: 1→7.097 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 197 10.06 %
Rwork0.186 1762 -
obs0.1883 1959 79.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 11 Å2 / Biso mean: 3.4905 Å2 / Biso min: 0.4 Å2
Refinement stepCycle: final / Resolution: 1→7.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60 0 0 0 60
Num. residues----8
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.0001-1.04550.2503230.220720679
1.0455-1.10040.215240.213621881
1.1004-1.1690.1409260.174223480
1.169-1.25880.2209250.202122880
1.2588-1.38470.1407230.194819977
1.3847-1.58310.2269270.181924682
1.5831-1.98730.1877220.155619877
1.9873-7.0970.2503270.183223378

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