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- PDB-5k2f: Structure of NNQQNY from yeast prion Sup35 with cadmium acetate d... -

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Basic information

Entry
Database: PDB / ID: 5k2f
TitleStructure of NNQQNY from yeast prion Sup35 with cadmium acetate determined by MicroED
ComponentsEukaryotic peptide chain release factor GTP-binding subunit
KeywordsPROTEIN FIBRIL / amyloid / yeast prion
Function / homology
Function and homology information


Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic stress granule / translation ...Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic stress granule / translation / GTPase activity / mRNA binding / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / : / Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1 Å
AuthorsRodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0445429 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01-AG029430 United States
Alzheimer's Disease Reasearch Center United States
Howard Hughes Medical Institute (HHMI) United States
Giannini Foundation United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.
Authors: Michael R Sawaya / Jose Rodriguez / Duilio Cascio / Michael J Collazo / Dan Shi / Francis E Reyes / Johan Hattne / Tamir Gonen / David S Eisenberg /
Abstract: Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This ...Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Oct 19, 2016Group: Database references
Revision 1.4Nov 30, 2016Group: Refinement description
Revision 1.5Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.6Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.7Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Jun 30, 2021Group: Data collection / Derived calculations
Category: diffrn_detector / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_detector.detector / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._diffrn_detector.detector / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.9Mar 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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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9513
Polymers7801
Non-polymers1712
Water1267
1
A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,12254
Polymers14,03618
Non-polymers3,08636
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation2_515-x,y-7/2,-z1
crystal symmetry operation2_525-x,y-5/2,-z1
crystal symmetry operation2_535-x,y-3/2,-z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_565-x,y+3/2,-z1
crystal symmetry operation2_575-x,y+5/2,-z1
crystal symmetry operation2_585-x,y+7/2,-z1
crystal symmetry operation2_595-x,y+9/2,-z1
Unit cell
Length a, b, c (Å)22.074, 4.932, 23.510
Angle α, β, γ (deg.)90.000, 104.290, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is an extended pair of beta sheets comprising peptides at positions X,Y,Z and -X,Y+1/2,-Z extended ad infinitum along the b crystal axis.

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Components

#1: Protein/peptide Eukaryotic peptide chain release factor GTP-binding subunit / SUP35 / ERF-3 / ERF3 / ERF2 / G1 to S phase transition protein 1 / Omnipotent suppressor protein 2 ...SUP35 / ERF-3 / ERF3 / ERF2 / G1 to S phase transition protein 1 / Omnipotent suppressor protein 2 / PSI no more protein 2 / Polypeptide release factor 3 / Translation release factor 3


Mass: 779.755 Da / Num. of mol.: 1 / Fragment: UNP residues 8-13 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05453
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Prion fibril composed of a 6-residue segment of Sup35 and cadmium
Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 3.25 kDa/nm / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
EM crystal formationInstrument: 24-well plate
Atmosphere: in air, in sealed chamber, in equilibrium with reservoir solution
Details: Crystals were grown by hanging-drop vapor diffusion at ~20 degrees C. The reservoir solution contained 100 mM HEPES, pH 7.0, and 1 M sodium acetate (pH not adjusted). Drops were prepared by ...Details: Crystals were grown by hanging-drop vapor diffusion at ~20 degrees C. The reservoir solution contained 100 mM HEPES, pH 7.0, and 1 M sodium acetate (pH not adjusted). Drops were prepared by pipetting 5 microliters of 30 mg/mL aqueous peptide solution, 4 microliters of reservoir solution, and 1 microliter of 0.1 M zinc sulfate onto a glass coverslip. Crystals grew within a day.
Lipid mixture: none / Temperature: 298 K / Time: 1 DAY
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 MHEPESC8H18N2O4S1
21.0 Msodium acetateNaC2H3O21
30.01 Mzinc sulfateZnSO41
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: crystal
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M cadmium sulfate

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 650 / Num. of grids imaged: 2
Details: The detector was operated in rolling shutter mode with 2x2 pixel binning.
Image scansSampling size: 15.6 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 1350 mm
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
1.71-901189.555910.1
1.36-1.712192.64.95780.1
1.19-1.363189.44.75340.1
1.08-1.194182.44.74960.1
1-1.0851663.33650.1
EM diffraction statsDetails: Phase statistics are not applicable. No imaging was used. The phases were obtained by a crystallographic direct methods program, SHELXD.
Fourier space coverage: 82.7 % / High resolution: 1 Å / Num. of intensities measured: 16753 / Num. of structure factors: 2399 / Phase error: 0.1 ° / Phase residual: 0.1 ° / Phase error rejection criteria: 0 / Rmerge: 15.1 / Rsym: 15.1
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Feb 3, 2016
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1→90 Å / Num. obs: 2564 / % possible obs: 84.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.18 / Χ2: 1.222 / Net I/av σ(I): 7.346 / Net I/σ(I): 5.1 / Num. measured all: 11810
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1-1.083.30.2823651.03866
1.08-1.194.70.2384961.10782.4
1.19-1.364.70.255341.10589.4
1.36-1.714.90.2455781.29692.6
1.71-9050.1395911.40489.5

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Processing

Software
NameVersionClassificationNB
DENZOdata collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
EM software
IDNameVersionCategoryDetails
1EM-Menu1image acquisition
5Denzo1.98.7diffraction indexing
6Coot0.8.2model fitting
7SHELXD2013/2otherphasing
8refmac55.8.0135model refinement
11SCALEPACK1.98.7crystallography merging
12SHELXD2013/23D reconstructiondirect methods
EM 3D crystal entity∠α: 90 ° / ∠β: 104.29 ° / ∠γ: 90 ° / A: 22.074 Å / B: 4.932 Å / C: 23.51 Å / Space group name: P1211 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Details: The density map was obtained using measured diffraction intensities and phases acquired from crystallographic direct methods program SHELXD.
Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 6.44 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum likelihood
RefinementResolution: 1→22.79 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.367 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 253 9.9 %RANDOM
Rwork0.2203 ---
obs0.2223 2308 80.97 %-
Displacement parametersBiso max: 22.93 Å2 / Biso mean: 6.444 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.36 Å2
2---0.29 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 0.98→22.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55 0 8 7 70
Biso mean--16.41 16.11 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0210.0258
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0040.0246
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.6881.89277
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.957399
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg5.52755
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg60.27828.3336
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg8.34158
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.1240.26
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0050.0281
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other00.0219
ELECTRON CRYSTALLOGRAPHYr_mcbond_it0.5020.50324
ELECTRON CRYSTALLOGRAPHYr_mcbond_other0.1890.44322
ELECTRON CRYSTALLOGRAPHYr_mcangle_it0.2330.67127
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr0.843104
ELECTRON CRYSTALLOGRAPHYr_sphericity_free6.51251
ELECTRON CRYSTALLOGRAPHYr_sphericity_bonded4.9455112
LS refinement shellResolution: 0.978→1.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 2 -
Rwork0.385 32 -
all-34 -
obs--15.6 %

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