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- EMDB-52433: Native human eIF2-eIF2B complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52433
TitleNative human eIF2-eIF2B complex
Map data
Sample
  • Complex: eIF2-eIF2B complex.
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Translation initiation factor eIF2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Translation initiation factor eIF2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsPhosphorylation / Eukaryotic Initiation Factor-2B / Eukaryotic Initiation Factor-2 / Translation Complex Catalytic Native / TRANSLATION
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 / 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 / formation of translation preinitiation complex / astrocyte development / guanyl-nucleotide exchange factor complex / eukaryotic 48S preinitiation complex / astrocyte differentiation / oligodendrocyte development / protein-synthesizing GTPase / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of translational initiation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / response to glucose / L13a-mediated translational silencing of Ceruloplasmin expression / ovarian follicle development / mitophagy / myelination / translation initiation factor binding / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / central nervous system development / hippocampus development / translational initiation / 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 / positive regulation of apoptotic process / cadherin binding / mRNA binding / GTPase activity / synapse / GTP binding / mitochondrion / RNA binding / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor eIF-2B subunit alpha, N-terminal / : / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal ...Translation initiation factor eIF-2B subunit alpha, N-terminal / : / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / 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 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / 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 / NagB/RpiA transferase-like / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Trimeric LpxA-like superfamily / 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 / Nucleotide-diphospho-sugar transferases / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / S1 domain / Armadillo-type fold / 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 / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesExpi293 (human) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: Termination of the integrated stress response.
Authors: Claudia De Miguel / Sigurdur R Thorkelsson / Agnieszka Fatalska / George Hodgson / Chao Wang / Anne Bertolotti /
Abstract: Stress responses enable cells to detect, adapt to, and survive challenges. The benefit of these signaling pathways depends on their reversibility. The integrated stress response (ISR) is elicited by ...Stress responses enable cells to detect, adapt to, and survive challenges. The benefit of these signaling pathways depends on their reversibility. The integrated stress response (ISR) is elicited by phosphorylation of translation initiation factor eIF2, which traps and inhibits rate-limiting translation factor eIF2B thereby attenuating translation initiation. Termination of this pathway thus requires relieving eIF2B from P-eIF2 inhibition. Here, we found that eIF2 phosphatase subunits PPP1R15A and PPP1R15B (R15B) bound P-eIF2 in complex with eIF2B. Biochemical investigations guided by cryo-EM structures of native eIF2-eIF2B and P-eIF2-eIF2B complexes bound to R15B demonstrated that R15B enabled dephosphorylation of otherwise dephosphorylation-incompetent P-eIF2 on eIF2B. This sheds light on ISR termination, revealing that R15B rescues eIF2B from P-eIF2 inhibition, thereby safeguarding translation and cell fitness.
History
DepositionDec 27, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52433.png

Downloads & links

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Map

FileDownload / File: emd_52433.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 494.4 Å		0.82 Å/pix.
x 600 pix.
= 494.4 Å		0.82 Å/pix.
x 600 pix.
= 494.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.29590768 - 0.77907217
Average (Standard dev.)-0.00052313606 (±0.016167568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 494.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52433_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_52433_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_52433_half_map_2.map
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Sample components

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Entire : eIF2-eIF2B complex.

EntireName: eIF2-eIF2B complex.
Components
  • Complex: eIF2-eIF2B complex.
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Translation initiation factor eIF2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Translation initiation factor eIF2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: eIF2-eIF2B complex.

SupramoleculeName: eIF2-eIF2B complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / Details: eIF2Bg subunits are bound to GTP.
Source (natural)Organism: Expi293 (human) / Location in cell: cytoplasm
Molecular weightTheoretical: 770 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: 2 / 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: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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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Macromolecule #3: Translation initiation factor eIF2B subunit epsilon

MacromoleculeName: Translation initiation factor eIF2B subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.466609 KDa
SequenceString: MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS KDQPRVLLPL ANVALIDYTL EFLTATGVQ ETFVFCCWKA AQIKEHLLKS KWCRPTSLNV VRIITSELYR SLGDVLRDVD AKALVRSDFL LVYGDVISNI N ITRALEEH ...String:
MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS KDQPRVLLPL ANVALIDYTL EFLTATGVQ ETFVFCCWKA AQIKEHLLKS KWCRPTSLNV VRIITSELYR SLGDVLRDVD AKALVRSDFL LVYGDVISNI N ITRALEEH RLRRKLEKNV SVMTMIFKES SPSHPTRCHE DNVVVAVDST TNRVLHFQKT QGLRRFAFPL SLFQGSSDGV EV RYDLLDC HISICSPQVA QLFTDNFDYQ TRDDFVRGLL VNEEILGNQI HMHVTAKEYG ARVSNLHMYS AVCADVIRRW VYP LTPEAN FTDSTTQSCT HSRHNIYRGP EVSLGHGSIL EENVLLGSGT VIGSNCFITN SVIGPGCHIG DNVVLDQTYL WQGV RVAAG AQIHQSLLCD NAEVKERVTL KPRSVLTSQV VVGPNITLPE GSVISLHPPD AEEDEDDGEF SDDSGADQEK DKVKM KGYN PAEVGAAGKG YLWKAAGMNM EEEEELQQNL WGLKINMEEE SESESEQSMD SEEPDSRGGS PQMDDIKVFQ NEVLGT LQR GKEENISCDN LVLEINSLKY AYNISLKEVM QVLSHVVLEF PLQQMDSPLD SSRYCALLLP LLKAWSPVFR NYIKRAA DH LEALAAIEDF FLEHEALGIS MAKVLMAFYQ LEILAEETIL SWFSQRDTTD KGQQLRKNQQ LQRFIQWLKE AEEESSED D

UniProtKB: Translation initiation factor eIF2B subunit epsilon

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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: 2 / 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: Translation initiation factor eIF2B subunit beta

MacromoleculeName: Translation initiation factor eIF2B subunit beta / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.039547 KDa
SequenceString: MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI ...String:
MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI GFSRTVEAFL KEAARKRKFH VIVAECAPFC QGHEMAVNLS KAGIETTVMT DAAIFAVMSR VNKVIIGTKT IL ANGALRA VTGTHTLALA AKHHSTPLIV CAPMFKLSPQ FPNEEDSFHK FVAPEEVLPF TEGDILEKVS VHCPVFDYVP PEL ITLFIS NIGGNAPSYI YRLMSELYHP DDHVL

UniProtKB: Translation initiation factor eIF2B subunit beta

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Macromolecule #6: Translation initiation factor eIF-2B subunit alpha

MacromoleculeName: Translation initiation factor eIF-2B subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.754148 KDa
SequenceString: MDDKELIEYF KSQMKEDPDM ASAVAAIRTL LEFLKRDKGE TIQGLRANLT SAIETLCGVD SSVAVSSGGE LFLRFISLAS LEYSDYSKC KKIMIERGEL FLRRISLSRN KIADLCHTFI KDGATILTHA YSRVVLRVLE AAVAAKKRFS VYVTESQPDL S GKKMAKAL ...String:
MDDKELIEYF KSQMKEDPDM ASAVAAIRTL LEFLKRDKGE TIQGLRANLT SAIETLCGVD SSVAVSSGGE LFLRFISLAS LEYSDYSKC KKIMIERGEL FLRRISLSRN KIADLCHTFI KDGATILTHA YSRVVLRVLE AAVAAKKRFS VYVTESQPDL S GKKMAKAL CHLNVPVTVV LDAAVGYIME KADLVIVGAE GVVENGGIIN KIGTNQMAVC AKAQNKPFYV VAESFKFVRL FP LNQQDVP DKFKYKADTL KVAQTGQDLK EEHPWVDYTA PSLITLLFTD LGVLTPSAVS DELIKLYL

UniProtKB: Translation initiation factor eIF2B subunit alpha

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Macromolecule #7: Translation initiation factor eIF-2B subunit delta

MacromoleculeName: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.640168 KDa
SequenceString: MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP ...String:
MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP TRKDYGSKVS LFSHLPQYSR QNSLTQFMSI PSSVIHPAMV RLGLQYSQGL VSGSNARCIA LLRALQQVIQ DY TTPPNEE LSRDLVNKLK PYMSFLTQCR PLSASMHNAI KFLNKEITSV GSSKREEEAK SELRAAIDRY VQEKIVLAAQ AIS RFAYQK ISNGDVILVY GCSSLVSRIL QEAWTEGRRF RVVVVDSRPW LEGRHTLRSL VHAGVPASYL LIPAASYVLP EVSK VLLGA HALLANGSVM SRVGTAQLAL VARAHNVPVL VCCETYKFCE RVQTDAFVSN ELDDPDDLQC KRGEHVALAN WQNHA SLRL LNLVYDVTPP ELVDLVITEL GMIPCSSVPV VLRVKSSDQ

UniProtKB: Translation initiation factor eIF2B subunit delta

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Macromolecule #8: Eukaryotic translation initiation factor 2 subunit 2

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / 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 #9: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, 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

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMTCEPtris(2-carboxyethyl)phosphine
100.0 mMKClpotassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 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
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9971 / Average exposure time: 3.0 sec. / 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: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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: 171151
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: 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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 256000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

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

PDB-9hve:
Native human eIF2-eIF2B complex

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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

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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

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