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- EMDB-12665: Cryo-EM structure of pre-dephosphorylation complex of phosphoryla... -

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Entry
Database: EMDB / ID: EMD-12665
TitleCryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)
Map dataUnsharpened GS-FSC map after corrected FSC-mask auto-tightening from non-uniform refinement in CryoSPARC. The contour level was set when opend in UCSF Chimera.
Sample
  • Complex: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
    • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
    • Protein or peptide: Deoxyribonuclease-1
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
  • Ligand: MANGANESE (II) ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsholophosphatase / PP1 / PPP1R15A / phosphorylated eIF2alpha / HYDROLASE
Function / homology
Function and homology information


fatty acid derivative binding / positive regulation of translational initiation in response to stress / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / eukaryotic initiation factor eIF2 binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling ...fatty acid derivative binding / positive regulation of translational initiation in response to stress / regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / eukaryotic initiation factor eIF2 binding / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / deoxyribonuclease I / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / PTW/PP1 phosphatase complex / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / protein phosphatase type 1 complex / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / deoxyribonuclease I activity / protein localization to endoplasmic reticulum / protein phosphatase 1 binding / neutrophil activation involved in immune response / regulation of translational initiation in response to stress / protein phosphatase regulator activity / eukaryotic 48S preinitiation complex / DNA catabolic process / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / cytoskeletal motor activator activity / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / glycogen metabolic process / calmodulin-dependent protein phosphatase activity / Ribosomal scanning and start codon recognition / myosin phosphatase activity / protein-serine/threonine phosphatase / myosin heavy chain binding / Translation initiation complex formation / tropomyosin binding / detection of maltose stimulus / entrainment of circadian clock by photoperiod / maltose transport complex / troponin I binding / filamentous actin / negative regulation of PERK-mediated unfolded protein response / mesenchyme migration / phosphatase activity / actin filament bundle / carbohydrate transport / actin filament bundle assembly / phosphoprotein phosphatase activity / protein phosphatase activator activity / skeletal muscle myofibril / positive regulation of signal transduction by p53 class mediator / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Response of EIF2AK4 (GCN2) to amino acid deficiency / transition metal ion binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / GTP hydrolysis and joining of the 60S ribosomal subunit / maltodextrin transmembrane transport / L13a-mediated translational silencing of Ceruloplasmin expression / mitophagy / stress fiber / skeletal muscle fiber development / protein dephosphorylation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / titin binding / actin filament polymerization / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / ATP-binding cassette (ABC) transporter complex / response to endoplasmic reticulum stress / Downregulation of TGF-beta receptor signaling / cell chemotaxis / filopodium / actin filament / translational initiation / circadian regulation of gene expression / regulation of circadian rhythm / PKR-mediated signaling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ABC-family proteins mediated transport / cytoplasmic stress granule
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal ...Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / S1 domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Actins signature 1. / Actin, conserved site / Actins signature 2. / Bacterial extracellular solute-binding protein / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Actin / Actin family / Actin / S1 domain / ATPase, nucleotide binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Protein phosphatase 1 regulatory subunit 15A / Deoxyribonuclease-1 / Eukaryotic translation initiation factor 2 subunit 1 / Maltose/maltodextrin-binding periplasmic protein / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit) / Bos taurus (domestic cattle) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsYan Y / Hardwick S
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome TrustWT 2008/Z/16/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Higher-order phosphatase-substrate contacts terminate the integrated stress response.
Authors: Yahui Yan / Heather P Harding / David Ron /
Abstract: Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally ...Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally affecting flexible access of the phosphopeptide to the active site. However, catalytic efficiency of holophosphatases towards their phosphoprotein substrates remains unexplained. Here we present a cryo-EM structure of the tripartite PP1c-PPP1R15A-G-actin holophosphatase that terminates signaling in the mammalian integrated stress response (ISR) in the pre-dephosphorylation complex with its substrate, translation initiation factor 2α (eIF2α). G-actin, whose essential role in eIF2α dephosphorylation is supported crystallographically, biochemically and genetically, aligns the catalytic and regulatory subunits, creating a composite surface that engages the N-terminal domain of eIF2α to position the distant phosphoserine-51 at the active site. Substrate residues that mediate affinity for the holophosphatase also make critical contacts with eIF2α kinases. Thus, a convergent process of higher-order substrate recognition specifies functionally antagonistic phosphorylation and dephosphorylation in the ISR.
History
DepositionMar 24, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-7nzm
  • Surface level: 0.05
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12665.png

Downloads & links

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Map

FileDownload / File: emd_12665.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened GS-FSC map after corrected FSC-mask auto-tightening from non-uniform refinement in CryoSPARC. The contour level was set when opend in UCSF Chimera.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 340 pix.
= 221.68 Å		0.65 Å/pix.
x 340 pix.
= 221.68 Å		0.65 Å/pix.
x 340 pix.
= 221.68 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.03137824 - 0.16581458
Average (Standard dev.)0.0011787033 (±0.007004136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 221.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6520.6520.652
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z221.680221.680221.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0310.1660.001

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Supplemental data

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Mask #1

Fileemd_12665_msk_1.map
Projections & Slices
AxesZYX

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Additional map: ResolveCyroEM map; 1.81rmsd (0.443e/A^3) in COOT

Fileemd_12665_additional_1.map
AnnotationResolveCyroEM map; 1.81rmsd (0.443e/A^3) in COOT
Projections & Slices
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Half map: half (A) map of the main map

Fileemd_12665_half_map_1.map
Annotationhalf (A) map of the main map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half (B) map of the main map

Fileemd_12665_half_map_2.map
Annotationhalf (B) map of the main map
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Sample components

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Entire : pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 w...

EntireName: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
Components
  • Complex: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
    • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
    • Protein or peptide: Deoxyribonuclease-1
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
  • Ligand: MANGANESE (II) ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 w...

SupramoleculeName: pre-dephosphorylation complex of phosphorylated eIF2alpha_2-187 with trapped holophosphatase (PP1A_D64A/PPP1R15A_553-624/G-actin)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: One copy of each component was present in the complex: phosphorylated eIF2alpha_2-187, PP1A_D64A, PPP1R15A_553-624, G-actin and DNase I. The full complex was purified by size exclusion chromatography.
Molecular weightTheoretical: 181 KDa

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Macromolecule #1: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.817863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PGLSCRFYQH KFPEVEDVVM VNVRSIAEMG AYVSLLEYNN IEGMILLSEL (SEP)RRRIRSINK LIRIGRNECV VVIRVD KEK GYIDLSKRRV SPEEAIKCED KFTKSKTVYS ILRHVAEVLE YTKDEQLESL FQRTAWVFDD KYKRPGYGAY DAFKHAV SD PSILDSLDLN EDEREVLINN INRRLTPQ

UniProtKB: Eukaryotic translation initiation factor 2 subunit 1

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Macromolecule #2: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

MacromoleculeName: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 33.647621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LNLDSIIGRL LEVQGSRPGK NVQLTENEIR GLCLKSREIF LSQPILLELE APLKICGAIH GQYYDLLRLF EYGGFPPESN YLFLGDYVD RGKQSLETIC LLLAYKIKYP ENFFLLRGNH ECASINRIYG FYDECKRRYN IKLWKTFTDC FNCLPIAAIV D EKIFCCHG ...String:
LNLDSIIGRL LEVQGSRPGK NVQLTENEIR GLCLKSREIF LSQPILLELE APLKICGAIH GQYYDLLRLF EYGGFPPESN YLFLGDYVD RGKQSLETIC LLLAYKIKYP ENFFLLRGNH ECASINRIYG FYDECKRRYN IKLWKTFTDC FNCLPIAAIV D EKIFCCHG GLSPDLQSME QIRRIMRPTD VPDQGLLCDL LWSDPDKDVQ GWGENDRGVS FTFGAEVVAK FLHKHDLDLI CR AHQVVED GYEFFAKRQL VTLFSAPNYC GEFDNAGAMM SVDETLMCSF QILKPAD

UniProtKB: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

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Macromolecule #3: Actin, alpha skeletal muscle, intermediate form

MacromoleculeName: Actin, alpha skeletal muscle, intermediate form / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.862613 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #4: Deoxyribonuclease-1

MacromoleculeName: Deoxyribonuclease-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 29.092574 KDa
SequenceString: LKIAAFNIRT FGETKMSNAT LASYIVRIVR RYDIVLIQEV RDSHLVAVGK LLDYLNQDDP NTYHYVVSEP LGRNSYKERY LFLFRPNKV SVLDTYQYDD GCESCGNDSF SREPAVVKFS SHSTKVKEFA IVALHSAPSD AVAEINSLYD VYLDVQQKWH L NDVMLMGD ...String:
LKIAAFNIRT FGETKMSNAT LASYIVRIVR RYDIVLIQEV RDSHLVAVGK LLDYLNQDDP NTYHYVVSEP LGRNSYKERY LFLFRPNKV SVLDTYQYDD GCESCGNDSF SREPAVVKFS SHSTKVKEFA IVALHSAPSD AVAEINSLYD VYLDVQQKWH L NDVMLMGD FNADCSYVTS SQWSSIRLRT SSTFQWLIPD SADTTATSTN CAYDRIVVAG SLLQSSVVPG SAAPFDFQAA YG LSNEMAL AISDHYPVEV TLT

UniProtKB: Deoxyribonuclease-1

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Macromolecule #5: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin...

MacromoleculeName: Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 49.169797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ARKVRFSEKV TVHFLAVWAG PAQAARQGPW EQLARDRSRF ARRITQAQEE LSPCLTPAAR ARAWARLRNP PLQAKIEEGK LVIWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF Q DKLYPFTW ...String:
ARKVRFSEKV TVHFLAVWAG PAQAARQGPW EQLARDRSRF ARRITQAQEE LSPCLTPAAR ARAWARLRNP PLQAKIEEGK LVIWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF Q DKLYPFTW DAVRYNGKLI AYPIAVEALS LIYNKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GG YAFKYEN GKYDIKDVGV DNAGAKAGLT FLVDLIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTV LPTFKG QPSKPFVGVL SAGINAASPN KELAKEFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQK GEIMP NIPQMSAFWY AVRTAVINAA SGRQTVDEAL KDAQTRITK

UniProtKB: Protein phosphatase 1 regulatory subunit 15A, Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
10.0 mMTris
150.0 mMNaCl
1.0 mMMnCl2
1.0 mMCaCl2
0.2 mMTCEP
0.2 mMATP
0.22 mMTriton X-100

Details: 0.22mM Triton X-100 was added into the solution before plunging.
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: OTHER / Details: current 25mA at Pelco EasiGLOW
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4025 / Average electron dose: 46.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.8000000000000003 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 132495
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: non-uniform refinement / Number images used: 60413
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Details: stochastic gradient descent (SGD) algorithm applied in CryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2a42

chain_id: A, source_name: PDB, initial_model_type: experimental model

2a42

chain_id: D, source_name: PDB, initial_model_type: experimental model

4mov

chain_id: B, source_name: PDB, initial_model_type: experimental model

1kl9

chain_id: E, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 47
Output model

PDB-7nzm:
Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)

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