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- EMDB-52434: Native human PPP1R15B-P-eIF2-eIF2B complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52434
TitleNative human PPP1R15B-P-eIF2-eIF2B complex
Map data
Sample
  • Complex: Local refinement of P-eIF2-eIF2B complex bound to R15B focused on an eIF2Bg and an eIF2g subunits.
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 15B
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
KeywordsTranslation / phosphorylation / Eukaryotic Initiation Factor-2B / Eukaryotic Initiation Factor-2
Function / homology
Function and homology information


male germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency ...male germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / negative regulation of translational initiation in response to stress / protein phosphatase type 1 complex / PERK-mediated unfolded protein response / PERK regulates gene expression / response to kainic acid / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / regulation of translational initiation in response to stress / translation factor activity, RNA binding / guanyl-nucleotide exchange factor complex / formation of translation preinitiation complex / protein phosphatase regulator activity / eukaryotic 48S preinitiation complex / oligodendrocyte development / protein-synthesizing GTPase / Formation of the ternary complex, and subsequently, the 43S complex / ER overload response / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of PERK-mediated unfolded protein response / negative regulation of protein phosphorylation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / response to glucose / mitophagy / translation initiation factor binding / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / translational initiation / response to hydrogen peroxide / response to peptide hormone / PKR-mediated signaling / ABC-family proteins mediated transport / male gonad development / cytoplasmic stress granule / cellular response to UV / T cell receptor signaling pathway / regulation of translation / cellular response to heat / ribosome binding / response to heat / cellular response to oxidative stress / in utero embryonic development / cadherin binding / GTPase activity / mRNA binding / synapse / GTP binding / endoplasmic reticulum / mitochondrion / RNA binding / extracellular exosome / zinc ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / : / EIF2B subunit epsilon LbH domain / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding ...Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / : / EIF2B subunit epsilon LbH domain / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / 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 / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Nucleotide-diphospho-sugar transferases / S1 domain / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit 3 / Protein phosphatase 1 regulatory subunit 15B / Translation initiation factor eIF2B subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDe Miguel C / Thorkelsson SR / Wang C / Bertolotti A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105185860 United Kingdom
Wellcome Trust206367/Z/ 17/Z United Kingdom
CitationJournal: Science / Year: 2025
Title: Local refinement of a P-eIF2-eIF2B complex bound to R15B.
Authors: De Miguel C / Thorkelsson SR / Wang C / Bertolotti A
History
DepositionDec 27, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52434.png

Downloads & links

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Map

FileDownload / File: emd_52434.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-1.1036949 - 1.7737758
Average (Standard dev.)0.00042396336 (±0.031001408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52434_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52434_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52434_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of P-eIF2-eIF2B complex bound to R15B focused on...

EntireName: Local refinement of P-eIF2-eIF2B complex bound to R15B focused on an eIF2Bg and an eIF2g subunits.
Components
  • Complex: Local refinement of P-eIF2-eIF2B complex bound to R15B focused on an eIF2Bg and an eIF2g subunits.
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 15B
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1

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Supramolecule #1: Local refinement of P-eIF2-eIF2B complex bound to R15B focused on...

SupramoleculeName: Local refinement of P-eIF2-eIF2B complex bound to R15B focused on an eIF2Bg and an eIF2g subunits.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: FLAG-R15B was expressed in Expi293 human cells and it immunopurified with a native P-eIF2-eIF2B complex.
Source (natural)Organism: Homo sapiens (human) / Location in cell: cytoplasm
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Translation initiation factor eIF-2B subunit gamma

MacromoleculeName: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.30423 KDa
SequenceString: MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL ...String:
MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL FMANEADLDE ELVIKGSILQ KHPRIRFHTG LVDAHLYCLK KYIVDFLMEN GSITSIRSEL IPYLVRKQFS SA SSQQGQE EKEEDLKKKE LKSLDIYSFI KEANTLNLAP YDACWNACRG DRWEDLSRSQ VRCYVHIMKE GLCSRVSTLG LYM EANRQV PKLLSALCPE EPPVHSSAQI VSKHLVGVDS LIGPETQIGE KSSIKRSVIG SSCLIKDRVT ITNCLLMNSV TVEE GSNIQ GSVICNNAVI EKGADIKDCL IGSGQRIEAK AKRVNEVIVG NDQLMEI

UniProtKB: Translation initiation factor eIF2B subunit gamma

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Macromolecule #2: Protein phosphatase 1 regulatory subunit 15B

MacromoleculeName: Protein phosphatase 1 regulatory subunit 15B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.927307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DYKDDDDKGD LPISARPACS NKLIDYILGG ASSDLETSSD PEGEDWDEEA EDDGFDSDSS LSDSDLEQDP EGLHLWNSFC SVDPYNPQN FTATIQTAAR IVPEEPSDSE

UniProtKB: Protein phosphatase 1 regulatory subunit 15B

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Macromolecule #3: Eukaryotic translation initiation factor 2 subunit 2

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.454484 KDa
SequenceString: MSGDEMIFDP TMSKKKKKKK KPFMLDEEGD TQTEETQPSE TKEVEPEPTE DKDLEADEED TRKKDASDDL DDLNFFNQKK KKKKTKKIF DIDEAEEGVK DLKIESDVQE PTEPEDDLDI MLGNKKKKKK NVKFPDEDEI LEKDEALEDE DNKKDDGISF S NQTGPAWA ...String:
MSGDEMIFDP TMSKKKKKKK KPFMLDEEGD TQTEETQPSE TKEVEPEPTE DKDLEADEED TRKKDASDDL DDLNFFNQKK KKKKTKKIF DIDEAEEGVK DLKIESDVQE PTEPEDDLDI MLGNKKKKKK NVKFPDEDEI LEKDEALEDE DNKKDDGISF S NQTGPAWA GSERDYTYEE LLNRVFNIMR EKNPDMVAGE KRKFVMKPPQ VVRVGTKKTS FVNFTDICKL LHRQPKHLLA FL LAELGTS GSIDGNNQLV IKGRFQQKQI ENVLRRYIKE YVTCHTCRSP DTILQKDTRL YFLQCETCHS RCSVASIKTG FQA VTGKRA QLRAKAN

UniProtKB: Eukaryotic translation initiation factor 2 subunit 2

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Macromolecule #4: Eukaryotic translation initiation factor 2 subunit 3

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-synthesizing GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.178406 KDa
SequenceString: MAGGEAGVTL GQPHLSRQDL TTLDVTKLTP LSHEVISRQA TINIGTIGHV AHGKSTVVKA ISGVHTVRFK NELERNITIK LGYANAKIY KLDDPSCPRP ECYRSCGSST PDEFPTDIPG TKGNFKLVRH VSFVDCPGHD ILMATMLNGA AVMDAALLLI A GNESCPQP ...String:
MAGGEAGVTL GQPHLSRQDL TTLDVTKLTP LSHEVISRQA TINIGTIGHV AHGKSTVVKA ISGVHTVRFK NELERNITIK LGYANAKIY KLDDPSCPRP ECYRSCGSST PDEFPTDIPG TKGNFKLVRH VSFVDCPGHD ILMATMLNGA AVMDAALLLI A GNESCPQP QTSEHLAAIE IMKLKHILIL QNKIDLVKES QAKEQYEQIL AFVQGTVAEG APIIPISAQL KYNIEVVCEY IV KKIPVPP RDFTSEPRLI VIRSFDVNKP GCEVDDLKGG VAGGSILKGV LKVGQEIEVR PGIVSKDSEG KLMCKPIFSK IVS LFAEHN DLQYAAPGGL IGVGTKIDPT LCRADRMVGQ VLGAVGALPE IFTELEISYF LLRRLLGVRT EGDKKAAKVQ KLSK NEVLM VNIGSLSTGG RVSAVKADLG KIVLTNPVCT EVGEKIALSR RVEKHWRLIG WGQIRRGVTI KPTVDDD

UniProtKB: Eukaryotic translation initiation factor 2 subunit 3

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Macromolecule #5: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.16118 KDa
SequenceString: MPGLSCRFYQ HKFPEVEDVV MVNVRSIAEM GAYVSLLEYN NIEGMILLSE LSRRRIRSIN KLIRIGRNEC VVVIRVDKEK GYIDLSKRR VSPEEAIKCE DKFTKSKTVY SILRHVAEVL EYTKDEQLES LFQRTAWVFD DKYKRPGYGA YDAFKHAVSD P SILDSLDL ...String:
MPGLSCRFYQ HKFPEVEDVV MVNVRSIAEM GAYVSLLEYN NIEGMILLSE LSRRRIRSIN KLIRIGRNEC VVVIRVDKEK GYIDLSKRR VSPEEAIKCE DKFTKSKTVY SILRHVAEVL EYTKDEQLES LFQRTAWVFD DKYKRPGYGA YDAFKHAVSD P SILDSLDL NEDEREVLIN NINRRLTPQA VKIRADIEVA CYGYEGIDAV KEALRAGLNC STENMPIKIN LIAPPRYVMT TT TLERTEG LSVLSQAMAV IKEKIEEKRG VFNVQMEPKV VTDTDETELA RQMERLEREN AEVDGDDDAE EMEAKAED

UniProtKB: Eukaryotic translation initiation factor 2 subunit 1

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMKClpotassium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GOLD / Support film - #0 - topology: HOLEY / Support film - #0 - Film thickness: 50 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 9438 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: An ab initio volume generated with cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167091
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9hvf:
Native human PPP1R15B-P-eIF2-eIF2B complex

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