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- EMDB-54610: Cryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex i... -

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Basic information

Entry
Database: EMDB / ID: EMD-54610
TitleCryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex in E1-ATP conformation in digitonin
Map data
Sample
  • Complex: EMC:Spf1 insertase:dislocase complex bound to ATPyS
    • Complex: ER membrane protein complex (EMC)
      • Protein or peptide: x 8 types
    • Complex: Spf1
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
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 / phospholipid transport / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / phosphatidylinositol-4-phosphate binding / protein hexamerization / phospholipid metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagosome assembly / protein unfolding / intracellular calcium ion homeostasis / transmembrane transport / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / metal ion binding / 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: 3.8 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 / Baydar I / Steigenberger S / von Gronau S / Arad S / Langlois C / Schuldiner M / Braeuning B / Schulman BA / Feige MJ
History
DepositionJul 30, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54610.png

Downloads & links

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Map

FileDownload / File: emd_54610.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 416 pix.
= 354.099 Å		0.85 Å/pix.
x 416 pix.
= 354.099 Å		0.85 Å/pix.
x 416 pix.
= 354.099 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.040685523 - 2.0834975
Average (Standard dev.)0.0011684444 (±0.023850877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 354.09918 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54610_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus Refinement map

Fileemd_54610_additional_1.map
AnnotationConsensus Refinement map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54610_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_54610_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : EMC:Spf1 insertase:dislocase complex bound to ATPyS

EntireName: EMC:Spf1 insertase:dislocase complex bound to ATPyS
Components
  • Complex: EMC:Spf1 insertase:dislocase complex bound to ATPyS
    • Complex: ER membrane protein complex (EMC)
      • Protein or peptide: ER membrane protein complex subunit 1
      • Protein or peptide: ER membrane protein complex subunit 2
      • 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: Endoplasmic reticulum membrane protein complex subunit 10
    • Complex: Spf1
      • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Digitonin

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Supramolecule #1: EMC:Spf1 insertase:dislocase complex bound to ATPyS

SupramoleculeName: EMC:Spf1 insertase:dislocase complex bound to ATPyS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

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Supramolecule #2: ER membrane protein complex (EMC)

SupramoleculeName: ER membrane protein complex (EMC) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

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Supramolecule #3: Spf1

SupramoleculeName: Spf1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 87.272938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTI DEIQLDSNDH NAMVCVNSSS NHWQKYDLHD WFLLEEGVDN APSTTILPQS SYLNDQVSIK NNELHILDEQ S KLAEWKLE ...String:
MKITCTDLVY VFILLFLNTS CVQAVFSDDA FITDWQLANL GPWEKVIPDS RDRNRVLILS NPTETSCLVS SFNVSSGQIL FRNVLPFTI DEIQLDSNDH NAMVCVNSSS NHWQKYDLHD WFLLEEGVDN APSTTILPQS SYLNDQVSIK NNELHILDEQ S KLAEWKLE LPQGFNKVEY FHREDPLALV LNVNDTQYMG FSANGTELIP VWQRDEWLTN VVDYAVLDVF DSRDVELNKD MK AELDSNS LWNAYWLRLT TNWNRLINLL KENQFSPGRV FTKLLALDAK DTTVSDLKFG FAKILIVLTH DGFIGGLDMV NKG QLIWKL DLEIDQGVKM FWTDKNHDEL VVFSHDGHYL TIEVTKDQPI IKSRSPLSER KTVDSVIRLN EHDHQYLIKF EDKD HLLFK LNPGKNTDVP IVANNHSSSH IFVTEHDTNG IYGYIIENDT VKQTWKKAVN SKEKMVAYSK RETTNLNTLG ITLGD KSVL YKYLYPNLAA YLIANEEHHT ITFNLIDTIT GEILITQEHK DSPDFRFPMD IVFGEYWVVY SYFSSEPVPE QKLVVV ELY ESLTPDERLS NSSDNFSYDP LTGHINKPQF QTKQFIFPEI IKTMSISKTT DDITTKAIVM ELENGQITYI PKLLLNA RG KPAEEMAKDK KKEFMATPYT PVIPINDNFI ITHFRNLLPG SDSQLISIPT NLESTSIICD LGLDVFCTRI TPSGQFDL M SPTFEKGKLL ITIFVLLVIT YFIRPSVSNK KLKSQWLIK

UniProtKB: ER membrane protein complex subunit 1

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Macromolecule #2: ER membrane protein complex subunit 2

MacromoleculeName: ER membrane protein complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 33.893211 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMV IMKATLLQIN GNDKGAIEYL ENLLNDDLEY ETDFVTYVSI AKKLIAIKTT SKNLSQESVL KEVVALTDKF P LDAELWWY ...String:
MLKDLVREKL LTIMNTKAYT QFNPEQLLQL ENEMKIYMKS GDSALTEGNY FFLMEMLFYV LVYRNQDVDA QVVYNTLRDR LGENSYKMV IMKATLLQIN GNDKGAIEYL ENLLNDDLEY ETDFVTYVSI AKKLIAIKTT SKNLSQESVL KEVVALTDKF P LDAELWWY ASEIYFEMGQ FEKACYCLEQ VLCITPFNYA CFGRLSETLY YEALRSKKQT KTELLEKALK NALRSVELSE LY LKGWALV NIISRELGRN KQNDLIKLSA SKLKEISAKS NNKDKITAEL ILNKI

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.372842 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLA KAKQQDGSQA GEVPNPFNDP SMSNAMMNMA KGNMASFIPQ TIIMWWVNHF FAGFILMQLP FPLTAKFKEM L QTGIICQD ...String:
MLLDDQLKYW VLLPISIVMV LTGVLKQYIM TLITGSSANE AQPRVKLTEW QYLQWAQLLI GNGGNLSSDA FAAKKEFLVK DLTEERHLA KAKQQDGSQA GEVPNPFNDP SMSNAMMNMA KGNMASFIPQ TIIMWWVNHF FAGFILMQLP FPLTAKFKEM L QTGIICQD LDVRWVSSIS WYFISVLGLN PVYNLIGLND QDMGIQAGIG GPQGPQGPPQ SQVDKAMHAM ANDLTIIQHE TC LDNVEQR VLKQYM

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.478721 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSEQEPYEWA KHLLDTKYIE KYNIQNSNTL PSPPGFEGNS SKGNVTRKQQ DATSQTTSLA QKNQITVLQV QKAWQIALQP AKSIPMNIF MSYMSGTSLQ IIPIMTALML LSGPIKAIFS TRSAFKPVLG NKATQSQVQT AMFMYIVFQG VLMYIGYRKL N SMGLIPNA KGDWLPWERI AHYNNGLQWF SD

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.799428 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSFVSKLLYT VSALVLFHSG FSSYEFHHLL KLNSLNNAQG AISKLPKDIM YETYAGLILF VLAVFTSFEK LQYLPIESND GKIISQGNY LKEIALNKAT NVDNLIGSNP NGEIIFTPSF VDVHMKRKIC REWASNTVKK EKWSHPQFEK GGGSGGGSGG S AWSHPQFE 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 12.411359 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSSNEEVFTQ INATANVVDN KKRLLFVQDS SALVLGLVAG FLQIESVHGF IWFLILYNLI NVIYIVWICQ LQPGKFYQSP LHDIFFESF FREITGFVMA WTFGYALIG

UniProtKB: ER membrane protein complex subunit 6

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Macromolecule #7: Protein SOP4

MacromoleculeName: Protein SOP4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.627627 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTY YVMYPASMDF NLKPNRILIE FKNLENGTLQ LNAFKNFFGR EYFPSKDITY PEKLQSMKVH PYITVELLHK A PIRSYLQA ...String:
MFSQIVLLLS AFIYVASATA RRGTIKGRLD LAASNITGFV STRTSFKLYQ IGNFSTEYPY TSTTMFQDDE GNFEFANLPL NDGVNETTY YVMYPASMDF NLKPNRILIE FKNLENGTLQ LNAFKNFFGR EYFPSKDITY PEKLQSMKVH PYITVELLHK A PIRSYLQA RNVSIFSTGI VGNILNSRWK LAGVITLIAL VVFPIIVEKL DPETARAIRE EAKRKQREKY AAVASK

UniProtKB: Protein SOP4

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Macromolecule #8: Endoplasmic reticulum membrane protein complex subunit 10

MacromoleculeName: Endoplasmic reticulum membrane protein complex subunit 10
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.792824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLK YDLIVDVDED NEVKQVSLSY DETNDAITAT VRYPEAGPTA PVTKLKKKTK TYADKKASKN KDGSTAQFEE D EEVKEVSW ...String:
MLVRLLRVIL LASMVFCADI LQLSYSDDAK DAIPLGTFEI DSTSDGNVTV TTVNIQDVEV SGEYCLNAQI EGKLDMPCFS YMKLRTPLK YDLIVDVDED NEVKQVSLSY DETNDAITAT VRYPEAGPTA PVTKLKKKTK TYADKKASKN KDGSTAQFEE D EEVKEVSW FQKNWKMLLL GLLIYNFVAG SAKKQQQGGA GADQKTE

UniProtKB: Endoplasmic reticulum membrane protein complex subunit 10

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Macromolecule #9: Endoplasmic reticulum transmembrane helix translocase

MacromoleculeName: Endoplasmic reticulum transmembrane helix translocase / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 136.700188 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYST TKNVNEATHI LIYTTPNNGS DGIVEIQRVT EAGSLQTFFQ FQKKRFLWHE NEQVFSSPKF LVDESPKIGD F QKCKGHSG ...String:
MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYST TKNVNEATHI LIYTTPNNGS DGIVEIQRVT EAGSLQTFFQ FQKKRFLWHE NEQVFSSPKF LVDESPKIGD F QKCKGHSG DLTHLKRLYG ENSFDIPIPT FMELFKEHAV APLFVFQVFC VALWLLDEFW YYSLFNLFMI ISMEAAAVFQ RL TALKEFR TMGIKPYTIN VFRNKKWVAL QTNELLPMDL VSITRTAEES AIPCDLILLD GSAIVNEAML SGESTPLLKE SIK LRPSED NLQLDGVDKI AVLHGGTKAL QVTPPEHKSD IPPPPDGGAL AIVTKTGFET SQGSLVRVMI YSAERVSVDN KEAL MFILF LLIFAVIASW YVWVEGTKMG RIQSKLILDC ILIITSVVPP ELPMELTMAV NSSLAALAKF YVYCTEPFRI PFAGR IDVC CFDKTGTLTG EDLVFEGLAG ISADSENIRH LYSAAEAPES TILVIGAAHA LVKLEDGDIV GDPMEKATLK AVGWAV ERK NSNYREGTGK LDIIRRFQFS SALKRSASIA SHNDALFAAV KGAPETIRER LSDIPKNYDE IYKSFTRSGS RVLALAS KS LPKMSQSKID DLNRDDVESE LTFNGFLIFH CPLKDDAIET IKMLNESSHR SIMITGDNPL TAVHVAKEVG IVFGETLI L DRAGKSDDNQ LLFRDVEETV SIPFDPSKDT FDHSKLFDRY DIAVTGYALN ALEGHSQLRD LLRHTWVYAR VSPSQKEFL LNTLKDMGYQ TLMCGDGTND VGALKQAHVG IALLNGTEEG LKKLGEQRRL EGMKMMYIKQ TEFMARWNQP QPPVPEPIAH LFPPGPKNP HYLKALESKG TVITPEIRKA VEEANSKPVE VIKPNGLSEK KPADLASLLL NSAGDAQGDE APALKLGDAS C AAPFTSKL ANVSAVTNII RQGRCALVNT IQMYKILALN CLISAYSLSI IYMAGVKFGD GQATVSGLLL SVCFLSISRG KP LEKLSKQ RPQSGIFNVY IMGSILSQFA VHIATLVYIT TEIYKLEPRE PQVDLEKEFA PSLLNTGIFI IQLVQQVSTF AVN YQGEPF RENIRSNKGM YYGLLGVTGL ALASATEFLP ELNEAMKFVP MTDDFKIKLT LTLLLDFFGS WGVEHFFKFF FMDD KPSDI SVQQVKIASK GSSGDYKDDD DK

UniProtKB: Endoplasmic reticulum transmembrane helix translocase

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #12: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 12 / Number of copies: 1 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*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

Concentration4.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMKOAc
0.03 %Digitonin
2.0 mMATPyS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.62 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 33661
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7kra

source_name: PDB, initial_model_type: experimental model

1-v4

source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9s5u:
Cryo-EM structure of yeast EMC:Spf1 insertase:dislocase complex in E1-ATP conformation in digitonin

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