[English] 日本語
Yorodumi
- EMDB-0649: Electron cryo-microscopy of the eukaryotic translation initiation... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0649
TitleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to translation initiation factor 2 from Homo sapiens
Map dataTwo eIF2 bound to eIF2B
Sample
  • Complex: eIF2B bound to eIF2
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Translation initiation factor eiF2 beta-subunit
  • Ligand: 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
KeywordsTranslation initiation / TRANSLATION
Function / homology
Function and homology information


translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency ...translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / 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 / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / 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 / astrocyte development / oligodendrocyte development / eukaryotic 48S preinitiation complex / astrocyte differentiation / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / response to glucose / mitophagy / ovarian follicle development / translation initiation factor binding / translation initiation factor activity / myelination / stress granule assembly / cellular response to amino acid starvation / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / hippocampus development / central nervous system development / translational initiation / PKR-mediated signaling / ABC-family proteins mediated transport / response to peptide hormone / cytoplasmic stress granule / cellular response to UV / regulation of translation / T cell receptor signaling pathway / ribosome binding / cellular response to heat / response to heat / cellular response to oxidative stress / cadherin binding / positive regulation of apoptotic process / GTPase activity / synapse / GTP binding / mitochondrion / RNA binding / extracellular exosome / 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 / : / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family ...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 / : / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / 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. / 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 / 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 / : / 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 / S1 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 / 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 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsNguyen H / Kenner L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108523 United States
CitationJournal: Science / Year: 2019
Title: eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response.
Authors: Lillian R Kenner / Aditya A Anand / Henry C Nguyen / Alexander G Myasnikov / Carolin J Klose / Lea A McGeever / Jordan C Tsai / Lakshmi E Miller-Vedam / Peter Walter / Adam Frost /
Abstract: The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase ...The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a guanosine triphosphatase that becomes activated by eIF2B, a two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from a substrate into an inhibitor of eIF2B. We report cryo-electron microscopy structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's bipartite catalytic centers to catalyze nucleotide exchange. Phosphorylation refolds eIF2α, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequestering it into a nonproductive complex.
History
DepositionMar 8, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.327
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.327
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o81
  • Surface level: 0.327
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0649.png

Downloads & links

-
Map

FileDownload / File: emd_0649.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTwo eIF2 bound to eIF2B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. Å		0.82 Å/pix.
x 500 pix.
= 411. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.327 / Movie #1: 0.327
Minimum - Maximum-0.82193613 - 1.9078244
Average (Standard dev.)0.0003476412 (±0.058941033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 411.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z411.000411.000411.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.8221.9080.000

-
Supplemental data

-
Sample components

+
Entire : eIF2B bound to eIF2

EntireName: eIF2B bound to eIF2
Components
  • Complex: eIF2B bound to eIF2
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
    • Protein or peptide: Translation initiation factor eiF2 beta-subunit
  • Ligand: 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide

+
Supramolecule #1: eIF2B bound to eIF2

SupramoleculeName: eIF2B bound to eIF2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Translation initiation factor eIF-2B subunit epsilon / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.366531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 LQK GKEENISCDN LVLEINSLKY AYNISLKEVM QVLSHVVLEF PLQQMDSPLD SSRYCALLLP LLKAWSPVFR NYIKRAA DH LEALAAIEDF FLEHEALGIS MAKVLMAFYQ LEILAGETIL SWFSQRDTTD KGQQLRKNQQ LQRFIQWLKE AEEESSED D

UniProtKB: Translation initiation factor eIF2B subunit epsilon

+
Macromolecule #2: Translation initiation factor eIF-2B subunit beta

MacromoleculeName: Translation initiation factor eIF-2B subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.008578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGGG SENLYFQSPG SAAKGSELSE RIESFVETLK RGGGPRSSEE MARETLGLLR QIITDHRWSN AGELMELIRR EGRRMTAAQ PSETTVGNMV RRVLKIIREE YGRLHGRSDE SDQQESLHKL LTSGGLNEDF SFHYAQLQSN IIEAINELLV E LEGTMENI ...String:
MHHHHHHGGG SENLYFQSPG SAAKGSELSE RIESFVETLK RGGGPRSSEE MARETLGLLR QIITDHRWSN AGELMELIRR EGRRMTAAQ PSETTVGNMV RRVLKIIREE YGRLHGRSDE SDQQESLHKL LTSGGLNEDF SFHYAQLQSN IIEAINELLV E LEGTMENI AAQALEHIHS NEVIMTIGFS RTVEAFLKEA ARKRKFHVIV AECAPFCQGH EMAVNLSKAG IETTVMTDAA IF AVMSRVN KVIIGTKTIL ANGALRAVTG THTLALAAKH HSTPLIVCAP MFKLSPQFPN EEDSFHKFVA PEEVLPFTEG DIL EKVSVH CPVFDYVPPE LITLFISNIG GNAPSYIYRL MSELYHPDDH VL

UniProtKB: Translation initiation factor eIF2B subunit beta

+
Macromolecule #3: Translation initiation factor eIF-2B subunit delta

MacromoleculeName: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.640168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

+
Macromolecule #4: Translation initiation factor eIF-2B subunit alpha

MacromoleculeName: Translation initiation factor eIF-2B subunit alpha / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.754148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

+
Macromolecule #5: Translation initiation factor eIF-2B subunit gamma

MacromoleculeName: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.30423 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

+
Macromolecule #6: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.16118 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

+
Macromolecule #7: Eukaryotic translation initiation factor 2 subunit 3

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.150422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 PGIVSKASEG KLMCKPKFSK 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

+
Macromolecule #8: Translation initiation factor eiF2 beta-subunit

MacromoleculeName: Translation initiation factor eiF2 beta-subunit / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.209482 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

+
Macromolecule #9: 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylami...

MacromoleculeName: 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
type: ligand / ID: 9 / Number of copies: 1 / Formula: C7B
Molecular weightTheoretical: 451.343 Da
Chemical component information

ChemComp-C7B:
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide / inhibitor*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11640
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more