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- EMDB-4544: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (map 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-4544
TitleStructure of eIF2B-eIF2 (phosphorylated at Ser51) complex (map 2)
Map dataFor optimal visualization of all eIF2 alpha and gamma and beta, gauss-filter the map by 1.34 and display it at 0.025 contour level
Sample
  • Complex: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit alpha
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit beta
Function / homology
Function and homology information


negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation ...negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / guanyl-nucleotide exchange factor complex / formation of translation preinitiation complex / positive regulation of cellular response to amino acid starvation / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of translational initiation / enzyme regulator activity / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / translational initiation / cytoplasmic stress granule / ribosome binding / ribosome / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Methylthioribose-1-phosphate isomerase, N-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 / : / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal ...Methylthioribose-1-phosphate isomerase, N-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 / : / : / 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. / 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
Translation initiation factor eIF2B subunit gamma / Eukaryotic translation initiation factor 2 subunit beta / Translation initiation factor eIF2B subunit delta / Translation initiation factor eIF2B subunit alpha / Eukaryotic translation initiation factor 2 subunit alpha / Eukaryotic translation initiation factor 2 subunit gamma / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsLlacer JL / Gordiyenko Y / Ramakrishnan V
Funding support United Kingdom, Spain, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Spanish Ministry of Economy and CompetitivenessBFU2017-85814-P Spain
Wellcome TrustWT096570 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the inhibition of translation through eIF2α phosphorylation.
Authors: Yuliya Gordiyenko / José Luis Llácer / V Ramakrishnan /
Abstract: One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of ...One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58-63 with eIF2Bδ leading to a competition with Met-tRNA.
History
Header (metadata) releaseAug 24, 2016-
DepositionJan 10, 2019-
Map releaseJun 26, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qg1
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4544.png

Downloads & links

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Map

FileDownload / File: emd_4544.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFor optimal visualization of all eIF2 alpha and gamma and beta, gauss-filter the map by 1.34 and display it at 0.025 contour level
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.26078832 - 0.4160329
Average (Standard dev.)-0.00008469851 (±0.010129743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z375.200375.200375.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.2610.416-0.000

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Supplemental data

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Half map: #2

Fileemd_4544_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4544_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)

EntireName: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)
Components
  • Complex: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)
    • Protein or peptide: Translation initiation factor eIF-2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF-2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF-2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit alpha
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit gamma
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit beta

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Supramolecule #1: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)

SupramoleculeName: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 837 KDa

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

MacromoleculeName: Translation initiation factor eIF-2B subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.062027 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSEFNITETY LRFLEEDTEM TMPIAAIEAL VTLLRIKTPE TAAEMINTIK SSTEELIKSI PNSVSLRAGC DIFMRFVLRN LHLYGDWEN CKQHLIENGQ LFVSRAKKSR NKIAEIGVDF IADDDIILVH GYSRAVFSLL NHAANKFIRF RCVVTESRPS K QGNQLYTL ...String:
MSEFNITETY LRFLEEDTEM TMPIAAIEAL VTLLRIKTPE TAAEMINTIK SSTEELIKSI PNSVSLRAGC DIFMRFVLRN LHLYGDWEN CKQHLIENGQ LFVSRAKKSR NKIAEIGVDF IADDDIILVH GYSRAVFSLL NHAANKFIRF RCVVTESRPS K QGNQLYTL LEQKGIPVTL IVDSAVGAVI DKVDKVFVGA EGVAESGGII NLVGTYSVGV LAHNARKPFY VVTESHKFVR MF PLSSDDL PMAGPPLDFT RRTDDLEDAL RGPTIDYTAQ EYITALITDL GVLTPSAVSE ELIKMWYD

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 42.621441 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSQAFTSVH PNAATSDVNV TIDTFVAKLK RRQVQGSYAI ALETLQLLMR FISAARWNHV NDLIEQIRDL GNSLEKAHPT AFSCGNVIR RILAVLRDEV EEDTMSTTVT STSVAEPLIS SMFNLLQKPE QPHQNRKNSS GSSSMKTKTD YRQVAIQGIK D LIDEIKNI ...String:
MSSQAFTSVH PNAATSDVNV TIDTFVAKLK RRQVQGSYAI ALETLQLLMR FISAARWNHV NDLIEQIRDL GNSLEKAHPT AFSCGNVIR RILAVLRDEV EEDTMSTTVT STSVAEPLIS SMFNLLQKPE QPHQNRKNSS GSSSMKTKTD YRQVAIQGIK D LIDEIKNI DEGIQQIAID LIHDHEILLT PTPDSKTVLK FLITARERSN RTFTVLVTEG FPNNTKNAHE FAKKLAQHNI ET LVVPDSA VFALMSRVGK VIIGTKAVFV NGGTISSNSG VSSVCECARE FRTPVFAVAG LYKLSPLYPF DVEKFVEFGG SQR ILPRMD PRKRLDTVNQ ITDYVPPENI DIYITNVGGF NPSFIYRIAW DNYKQIDVHL DKNKA

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

MacromoleculeName: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 65.76832 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSIQAFVFCG KGSNLAPFTQ PDFPFQTQNK DSTAATSGDK LNELVNSALD STVINEFMQH STRLPKALLP IGNRPMIEYV LDWCDQADF KEISVVAPVD EIELIESGLT SFLSLRKQQF ELIYKALSNS NHSHHLQDPK KINFIPSKAN STGESLQKEL L PRINGDFV ...String:
MSIQAFVFCG KGSNLAPFTQ PDFPFQTQNK DSTAATSGDK LNELVNSALD STVINEFMQH STRLPKALLP IGNRPMIEYV LDWCDQADF KEISVVAPVD EIELIESGLT SFLSLRKQQF ELIYKALSNS NHSHHLQDPK KINFIPSKAN STGESLQKEL L PRINGDFV ILPCDFVTDI PPQVLVDQFR NRDDNNLAMT IYYKNSLDSS IDKKQQQKQK QQQFFTVYSE NEDSERQPIL LD VYSQRDV TKTKYLQIRS HLLWNYPNLT VSTKLLNSFI YFCSFELCQL LKLGPQSMSR QASFKDPFTG NQQQQNPPTT DDD EDRNHD DDDDYKPSAT SIQPTYFKKK NDLILDPINC NKSLSKVFRD LSRRSWQHSK PREPIGIFIL PNETLFIRAN NLNA YMDAN RFVLKIKSQT MFTKNIQIQS AAIGADAIVD PKCQISAHSN VKMSVLGTQA NIGSRCRVAG SLLFPGVHLG DEVIL ENCI IGPMAKIGSK CKLSNCYIEG HYVVEPKNNF KGETLANVYL DEDEEDELIY DDSVIAGESE IAEETDSDDR SDEDSD DSE YTDEYEYEDD GLFER

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

MacromoleculeName: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 70.945195 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSESEAKSRS ATPPSKAKQA TPTTTAAANG EKKLTNKELK ELKKQEKAAK RAAMKQANGI SIEQQQQQAQ MKKEKKQLQR EQQQKREQK QKNANKKKQN ERNVKKSTLF GHLETTEERR ATILALTSAV SSPKTSRITA AGLMVPVVAS ALSGSNVLTA S SLMPVGPN ...String:
MSESEAKSRS ATPPSKAKQA TPTTTAAANG EKKLTNKELK ELKKQEKAAK RAAMKQANGI SIEQQQQQAQ MKKEKKQLQR EQQQKREQK QKNANKKKQN ERNVKKSTLF GHLETTEERR ATILALTSAV SSPKTSRITA AGLMVPVVAS ALSGSNVLTA S SLMPVGPN ASSTVSASAP ASTTTTLPAS SAALSAGTSS ASTNTPTAIQ QEIASSNASD VAKTLASISL EAGEFNVIPG IS SVIPTVL EQSFDNSSLI SSVKELLLNK DLIHPSILLL TSHLAHYKIV GSIPRCIAML EVFQIVIKDY QTPKGTTLSR NLT SYLSHQ IDLLKKARPL SVTMGNAIRW LKQEISLIDP STPDKAAKKD LCEKIGQFAK EKIELADQLI IDNASTQIEE STTI VTYGS SKVLTELLLH NAISLKKNIK VIVVDSRPLF EGRKMAETLR NAGVNVMYAL ITSLDTIFNM DVDYVFLGAH SILSN GFLY SRAGTAMLAM SAKRRNIPVL VCCESLKFSQ RVQLDSVTFN ELADPNDLVN IDYENPVERR GNKGALLNQF IKERKF EKK KLAMENKPKG NKIGGKKGSE GESKDASNEE DSNSKNILDG WQELPSLNIV NILYDLTPPE YIKKVITEFG ALPPSSV PV ILREYKGSA

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

MacromoleculeName: Translation initiation factor eIF-2B subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 81.249062 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAGKKGQKKS GLGNHGKNSD MDVEDRLQAV VLTDSYETRF MPLTAVKPRC LLPLANVPLI EYTLEFLAKA GVHEVFLICS SHANQINDY IENSKWNLPW SPFKITTIMS PEARCTGDVM RDLDNRGIIT GDFILVSGDV LTNIDFSKML EFHKKMHLQD K DHISTMCL ...String:
MAGKKGQKKS GLGNHGKNSD MDVEDRLQAV VLTDSYETRF MPLTAVKPRC LLPLANVPLI EYTLEFLAKA GVHEVFLICS SHANQINDY IENSKWNLPW SPFKITTIMS PEARCTGDVM RDLDNRGIIT GDFILVSGDV LTNIDFSKML EFHKKMHLQD K DHISTMCL SKASTYPKTR TIEPAAFVLD KSTSRCIYYQ DLPLPSSREK TSIQIDPELL DNVDEFVIRN DLIDCRIDIC TS HVPLIFQ ENFDYQSLRT DFVKGVISSD ILGKHIYAYL TDEYAVRVES WQTYDTISQD FLGRWCYPLV LDSNIQDDQT YSY ESRHIY KEKDVVLAQS CKIGKCTAIG SGTKIGEGTK IENSVIGRNC QIGENIRIKN SFIWDDCIIG NNSIIDHSLI ASNA TLGSN VRLNDGCIIG FNVKIDDNMD LDRNTKISAS PLKNAGSRMY DNESNEQFDQ DLDDQTLAVS IVGDKGVGYI YESEV SDDE DSSTEACKEI NTLSNQLDEL YLSDDSISSA TKKTKKRRTM SVNSIYTDRE EIDSEFEDED FEKEGIATVE RAMENN HDL DTALLELNTL RMSMNVTYHE VRIATITALL RRVYHFIATQ TLGPKDAVVK VFNQWGLLFK RQAFDEEEYI DLMNIIM EK IVEQSFDKPD LILFSALVSL YDNDIIEEDV IYKWWDNVST DPRYDEVKKL TVKWVEWLQN ADEESSSEEE

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Macromolecule #6: Eukaryotic translation initiation factor 2 subunit alpha

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit alpha
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 34.843633 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSTSHCRFYE NKYPEIDDIV MVNVQQIAEM GAYVKLLEYD NIEGMILLSE L(SEP)RRRIRSIQ KLIRVGKNDV AVVLRV DKE KGYIDLSKRR VSSEDIIKCE EKYQKSKTVH SILRYCAEKF QIPLEELYKT IAWPLSRKFG HAYEAFKLSI IDETVWE GI EPPSKDVLDE ...String:
MSTSHCRFYE NKYPEIDDIV MVNVQQIAEM GAYVKLLEYD NIEGMILLSE L(SEP)RRRIRSIQ KLIRVGKNDV AVVLRV DKE KGYIDLSKRR VSSEDIIKCE EKYQKSKTVH SILRYCAEKF QIPLEELYKT IAWPLSRKFG HAYEAFKLSI IDETVWE GI EPPSKDVLDE LKNYISKRLT PQAVKIRADV EVSCFSYEGI DAIKDALKSA EDMSTEQMQV KVKLVAAPLY VLTTQALD K QKGIEQLESA IEKITEVITK YGGVCNITMP PKAVTATEDA ELQALLESKE LDNRSDSEDD EDESDDE

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Macromolecule #7: Eukaryotic translation initiation factor 2 subunit gamma

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit gamma
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.942699 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDLQDQEPS IIINGNLEPV GEPDIVEETE VVAQETQETQ DADKPKKKVA FTGLEEDGET EEEKRKREFE EGGGLPEQPL NPDFSKLNP LSAEIINRQA TINIGTIGHV AHGKSTVVRA ISGVQTVRFK DELERNITIK LGYANAKIYK CQEPTCPEPD C YRSFKSDK ...String:
MSDLQDQEPS IIINGNLEPV GEPDIVEETE VVAQETQETQ DADKPKKKVA FTGLEEDGET EEEKRKREFE EGGGLPEQPL NPDFSKLNP LSAEIINRQA TINIGTIGHV AHGKSTVVRA ISGVQTVRFK DELERNITIK LGYANAKIYK CQEPTCPEPD C YRSFKSDK EISPKCQRPG CPGRYKLVRH VSFVDCPGHD ILMSTMLSGA AVMDAALLLI AGNESCPQPQ TSEHLAAIEI MK LKHVIIL QNKVDLMREE SALEHQKSIL KFIRGTIADG APIVPISAQL KYNIDAVNEF IVKTIPVPPR DFMISPRLIV IRS FDVNKP GAEIEDLKGG VAGGSILNGV FKLGDEIEIR PGIVTKDDKG KIQCKPIFSN IVSLFAEQND LKFAVPGGLI GVGT KVDPT LCRADRLVGQ VVGAKGHLPN IYTDIEINYF LLRRLLGVKT DGQKQAKVRK LEPNEVLMVN IGSTATGARV VAVKA DMAR LQLTSPACTE INEKIALSRR IEKHWRLIGW ATIKKGTTLE PIA

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Macromolecule #8: Eukaryotic translation initiation factor 2 subunit beta

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit beta
type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 31.631309 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSDLAAELG FDPALKKKKK TKKVIPDDFD AAVNGKENGS GDDLFAGLKK KKKKSKSVSA DAEAEKEPTD DIAEALGELS LKKKKKKTK DSSVDAFEKE LAKAGLDNVD AESKEGTPSA NSSIQQEVGL PYSELLSRFF NILRTNNPEL AGDRSGPKFR I PPPVCLRD ...String:
MSSDLAAELG FDPALKKKKK TKKVIPDDFD AAVNGKENGS GDDLFAGLKK KKKKSKSVSA DAEAEKEPTD DIAEALGELS LKKKKKKTK DSSVDAFEKE LAKAGLDNVD AESKEGTPSA NSSIQQEVGL PYSELLSRFF NILRTNNPEL AGDRSGPKFR I PPPVCLRD GKKTIFSNIQ DIAEKLHRSP EHLIQYLFAE LGTSGSVDGQ KRLVIKGKFQ SKQMENVLRR YILEYVTCKT CK SINTELK REQSNRLFFM VCKSCGSTRS VSSIKTGFQA TVGKRRRM

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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

Concentration0.17 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
5.0 mMMagnessium chloride
100.0 mMPotassium chloride
5.0 mMbeta mercaptoethanol
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 100.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Number grids imaged: 3 / Number real images: 4523 / Average electron dose: 45.0 e/Å2
Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in ...Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in integrating mode 1.1 sec images were recorded (dose 45e-/A2)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
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

DetailsFEI Falcon III
Particle selectionNumber selected: 633220
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5b04


Details: Low pass filtered to 60 angstrom
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 183468
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)

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Atomic model buiding 1

Initial model(PDB ID:

5b04

,

6fyx

)
RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: FSC
Output model

PDB-6qg1:
Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2)

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