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- EMDB-54652: Cryo-EM structure of endogenous yeast EMC in complex with Spf1 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-54652
TitleCryo-EM structure of endogenous yeast EMC in complex with Spf1 in digitonin
Map data
Sample
  • Complex: endogenous yeast EMC bound to Spf1
    • Protein or peptide: ER membrane protein complex subunit 1
    • Protein or peptide: ER membrane protein complex subunit
    • Protein or peptide: ER membrane protein complex subunit 3
    • Protein or peptide: ER membrane protein complex subunit 4
    • Protein or peptide: ER membrane protein complex subunit 5
    • Protein or peptide: ER membrane protein complex subunit 6
    • Protein or peptide: Protein Sop4
    • Protein or peptide: ER membrane protein complex subunit 10
    • Protein or peptide: ER transmembrane helix dislocase
KeywordsER membrane protein complex / protein translocation / protein folding / chaperone / membrane proteins / MEMBRANE PROTEIN
Function / homology
Function and homology information


extraction of mislocalized protein from ER membrane / EMC complex / Ion transport by P-type ATPases / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / sterol homeostasis / membrane protein dislocase activity / tail-anchored membrane protein insertion into ER membrane / intracellular manganese ion homeostasis / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate ...extraction of mislocalized protein from ER membrane / EMC complex / Ion transport by P-type ATPases / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / sterol homeostasis / membrane protein dislocase activity / tail-anchored membrane protein insertion into ER membrane / intracellular manganese ion homeostasis / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / protein folding in endoplasmic reticulum / ATPase-coupled monoatomic cation transmembrane transporter activity / phospholipid transport / cis-Golgi network / phosphatidylinositol-4-phosphate binding / protein hexamerization / phospholipid metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagosome assembly / protein unfolding / transmembrane transport / intracellular calcium ion homeostasis / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / nucleus
Similarity search - Function
Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 ...Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, second beta-propeller / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / : / : / P5A-ATPase, transmembrane helical hairpin / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / P-type ATPase, subfamily V / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / TPR repeat profile. / Tetratricopeptide repeat / HAD superfamily / HAD-like superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 1 / ER membrane protein complex subunit 3 / Protein SOP4 / Endoplasmic reticulum transmembrane helix translocase / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / Endoplasmic reticulum membrane protein complex subunit 10 / ER membrane protein complex subunit 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsKlose CJ / Prabu JR / Schulman BA
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 1581/5-1 Germany
European Research Council (ERC)101098161European Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structural basis of an endoplasmic reticulum EMC:Spf1 insertase-dislocase complex
Authors: Klose CJ / Prabu JR / Fenech EJ / Braeuning B / Baydar I / Steigenberger S / von Gronau S / Arad S / Langlois C / Schuldiner M / Schulman BA / Feige MJ
History
DepositionAug 5, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54652.png

Downloads & links

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Map

FileDownload / File: emd_54652.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 344 pix.
= 648.44 Å		1.89 Å/pix.
x 344 pix.
= 648.44 Å		1.89 Å/pix.
x 344 pix.
= 648.44 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00844
Minimum - Maximum-0.0099964915 - 0.04174957
Average (Standard dev.)0.00006974738 (±0.0009802213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 648.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54652_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_54652_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_54652_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54652_half_map_2.map
Projections & Slices
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Sample components

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Entire : endogenous yeast EMC bound to Spf1

EntireName: endogenous yeast EMC bound to Spf1
Components
  • Complex: endogenous yeast EMC bound to Spf1
    • Protein or peptide: ER membrane protein complex subunit 1
    • Protein or peptide: ER membrane protein complex subunit
    • Protein or peptide: ER membrane protein complex subunit 3
    • Protein or peptide: ER membrane protein complex subunit 4
    • Protein or peptide: ER membrane protein complex subunit 5
    • Protein or peptide: ER membrane protein complex subunit 6
    • Protein or peptide: Protein Sop4
    • Protein or peptide: ER membrane protein complex subunit 10
    • Protein or peptide: ER transmembrane helix dislocase

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Supramolecule #1: endogenous yeast EMC bound to Spf1

SupramoleculeName: endogenous yeast EMC bound to Spf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ER membrane protein complex subunit 1

MacromoleculeName: ER membrane protein complex subunit 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTID EIQLDSNDHN AMVCVNSSSN HWQKYDLHDW FLLEEGVDNA PSTTILPQSS YLNDQVSIKN NELHILDEQS KLAEWKLELP ...String:
MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTID EIQLDSNDHN AMVCVNSSSN HWQKYDLHDW FLLEEGVDNA PSTTILPQSS YLNDQVSIKN NELHILDEQS KLAEWKLELP QGFNKVEYFH REDPLALVLN VNDTQYMGFS ANGTELIPVW QRDEWLTNVV DYAVLDVFDS RDVELNKDMK AELDSNSLWN AYWLRLTTNW NRLINLLKEN QFSPGRVFTK LLALDAKDTT VSDLKFGFAK ILIVLTHDGF IGGLDMVNKG QLIWKLDLEI DQGVKMFWTD KNHDELVVFS HDGHYLTIEV TKDQPIIKSR SPLSERKTVD SVIRLNEHDH QYLIKFEDKD HLLFKLNPGK NTDVPIVANN HSSSHIFVTE HDTNGIYGYI IENDTVKQTW KKAVNSKEKM VAYSKRETTN LNTLGITLGD KSVLYKYLYP NLAAYLIANE EHHTITFNLI DTITGEILIT QEHKDSPDFR FPMDIVFGEY WVVYSYFSSE PVPEQKLVVV ELYESLTPDE RLSNSSDNFS YDPLTGHINK PQFQTKQFIF PEIIKTMSIS KTTDDITTKA IVMELENGQI TYIPKLLLNA RGKPAEEMAK DKKKEFMATP YTPVIPINDN FIITHFRNLL PGSDSQLISI PTNLESTSII CDLGLDVFCT RITPSGQFDL MSPTFEKGKL LITIFVLLVI TYFIRPSVSN KKLKSQWLIK

UniProtKB: ER membrane protein complex subunit 1

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Macromolecule #2: ER membrane protein complex subunit

MacromoleculeName: ER membrane protein complex subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMVI MKATLLQING NDKGAIEYLE NLLNDDLEYE TDFVTYVSIA KKLIAIKTTS KNLSQESVLK EVVALTDKFP LDAELWWYAS ...String:
MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMVI MKATLLQING NDKGAIEYLE NLLNDDLEYE TDFVTYVSIA KKLIAIKTTS KNLSQESVLK EVVALTDKFP LDAELWWYAS EIYFEMGQFE KACYCLEQVL CITPFNYACF GRLSETLYYE ALRSKKQTKT ELLEKALKNA LRSVELSELY LKGWALVNII SRELGRNKQN DLIKLSASKL KEISAKSNNK DKITAELILN KI

UniProtKB: ER membrane protein complex subunit 2

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Macromolecule #3: ER membrane protein complex subunit 3

MacromoleculeName: ER membrane protein complex subunit 3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLAK AKQQDGSQAG EVPNPFNDPS MSNAMMNMAK GNMASFIPQT IIMWWVNHFF AGFILMQLPF PLTAKFKEML QTGIICQDLD ...String:
MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLAK AKQQDGSQAG EVPNPFNDPS MSNAMMNMAK GNMASFIPQT IIMWWVNHFF AGFILMQLPF PLTAKFKEML QTGIICQDLD VRWVSSISWY FISVLGLNPV YNLIGLNDQD MGIQAGIGGP QGPQGPPQSQ VDKAMHAMAN DLTIIQHETC LDNVEQRVLK QYM

UniProtKB: ER membrane protein complex subunit 3

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Macromolecule #4: ER membrane protein complex subunit 4

MacromoleculeName: ER membrane protein complex subunit 4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSEQEPYEWA KHLLDTKYIE KYNIQNSNTL PSPPGFEGNS SKGNVTRKQQ DATSQTTSLA QKNQITVLQV QKAWQIALQP AKSIPMNIFM SYMSGTSLQI IPIMTALMLL SGPIKAIFST RSAFKPVLGN KATQSQVQTA MFMYIVFQGV LMYIGYRKLN SMGLIPNAKG DWLPWERIAH YNNGLQWFSD

UniProtKB: ER membrane protein complex subunit 4

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Macromolecule #5: ER membrane protein complex subunit 5

MacromoleculeName: ER membrane protein complex subunit 5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSFVSKLLYT VSALVLFHSG FSSYEFHHLL KLNSLNNAQG AISKLPKDIM YETYAGLILF VLAVFTSFEK LQYLPIESND GKIISQGNYL KEIALNKATN VDNLIGSNPN GEIIFTPSFV DVHMKRKICR EWASNTVKKE K

UniProtKB: ER membrane protein complex subunit 5

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Macromolecule #6: ER membrane protein complex subunit 6

MacromoleculeName: ER membrane protein complex subunit 6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSSNEEVFTQ INATANVVDN KKRLLFVQDS SALVLGLVAG FLQIESVHGF IWFLILYNLI NVIYIVWICQ LQPGKFYQSP LHDIFFESFF REITGFVMAW TFGYALIG

UniProtKB: ER membrane protein complex subunit 6

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Macromolecule #7: Protein Sop4

MacromoleculeName: Protein Sop4 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTYY VMYPASMDFN LKPNRILIEF KNLENGTLQL NAFKNFFGRE YFPSKDITYP EKLQSMKVHP YITVELLHKA PIRSYLQARN ...String:
MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTYY VMYPASMDFN LKPNRILIEF KNLENGTLQL NAFKNFFGRE YFPSKDITYP EKLQSMKVHP YITVELLHKA PIRSYLQARN VSIFSTGIVG NILNSRWKLA GVITLIALVV FPIIVEKLDP ETARAIREEA KRKQREKYAA VASK

UniProtKB: Protein SOP4

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Macromolecule #8: ER membrane protein complex subunit 10

MacromoleculeName: ER membrane protein complex subunit 10 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLKY DLIVDVDEDN EVKQVSLSYD ETNDAITATV RYPEAGPTAP VTKLKKKTKT YADKKASKNK DGSTAQFEED EEVKEVSWFQ ...String:
MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLKY DLIVDVDEDN EVKQVSLSYD ETNDAITATV RYPEAGPTAP VTKLKKKTKT YADKKASKNK DGSTAQFEED EEVKEVSWFQ KNWKMLLLGL LIYNFVAGSA KKQQQGGAGA DQKTE

UniProtKB: Endoplasmic reticulum membrane protein complex subunit 10

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Macromolecule #9: ER transmembrane helix dislocase

MacromoleculeName: ER transmembrane helix dislocase / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYSTT KNVNEATHIL IYTTPNNGSD GIVEIQRVTE AGSLQTFFQF QKKRFLWHEN EQVFSSPKFL VDESPKIGDF QKCKGHSGDL ...String:
MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYSTT KNVNEATHIL IYTTPNNGSD GIVEIQRVTE AGSLQTFFQF QKKRFLWHEN EQVFSSPKFL VDESPKIGDF QKCKGHSGDL THLKRLYGEN SFDIPIPTFM ELFKEHAVAP LFVFQVFCVA LWLLDEFWYY SLFNLFMIIS MEAAAVFQRL TALKEFRTMG IKPYTINVFR NKKWVALQTN ELLPMDLVSI TRTAEESAIP CDLILLDGSA IVNEAMLSGE STPLLKESIK LRPSEDNLQL DGVDKIAVLH GGTKALQVTP PEHKSDIPPP PDGGALAIVT KTGFETSQGS LVRVMIYSAE RVSVDNKEAL MFILFLLIFA VIASWYVWVE GTKMGRIQSK LILDCILIIT SVVPPELPME LTMAVNSSLA ALAKFYVYCT EPFRIPFAGR IDVCCFDKTG TLTGEDLVFE GLAGISADSE NIRHLYSAAE APESTILVIG AAHALVKLED GDIVGDPMEK ATLKAVGWAV ERKNSNYREG TGKLDIIRRF QFSSALKRSA SIASHNDALF AAVKGAPETI RERLSDIPKN YDEIYKSFTR SGSRVLALAS KSLPKMSQSK IDDLNRDDVE SELTFNGFLI FHCPLKDDAI ETIKMLNESS HRSIMITGDN PLTAVHVAKE VGIVFGETLI LDRAGKSDDN QLLFRDVEET VSIPFDPSKD TFDHSKLFDR YDIAVTGYAL NALEGHSQLR DLLRHTWVYA RVSPSQKEFL LNTLKDMGYQ TLMCGDGTND VGALKQAHVG IALLNGTEEG LKKLGEQRRL EGMKMMYIKQ TEFMARWNQP QPPVPEPIAH LFPPGPKNPH YLKALESKGT VITPEIRKAV EEANSKPVEV IKPNGLSEKK PADLASLLLN SAGDAQGDEA PALKLGDASC AAPFTSKLAN VSAVTNIIRQ GRCALVNTIQ MYKILALNCL ISAYSLSIIY MAGVKFGDGQ ATVSGLLLSV CFLSISRGKP LEKLSKQRPQ SGIFNVYIMG SILSQFAVHI ATLVYITTEI YKLEPREPQV DLEKEFAPSL LNTGIFIIQL VQQVSTFAVN YQGEPFRENI RSNKGMYYGL LGVTGLALAS ATEFLPELNE AMKFVPMTDD FKIKLTLTLL LDFFGSWGVE HFFKFFFMDD KPSDISVQQV KIASK

UniProtKB: Endoplasmic reticulum transmembrane helix translocase

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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

Concentration1.4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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