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- EMDB-21929: Human ER membrane protein complex in a lipid nanodisc, overall map -

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Basic information

Entry
Database: EMDB / ID: EMD-21929
TitleHuman ER membrane protein complex in a lipid nanodisc, overall mapEndoplasmic reticulum
Map data'Overall' human EMC post-processed, sharpened, and masked map.
Sample
  • Complex: Human ER Membrane Protein ComplexEndoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 1Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 2Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 3Endoplasmic reticulum
    • Protein or peptide: ER Membrane Protein Complex Subunit 4Endoplasmic reticulum
    • Protein or peptide: Membrane magnesium transporter 1
    • Protein or peptide: ER membrane protein complex subunit 6Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 7Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 8Endoplasmic reticulum
  • Protein or peptide: ER membrane protein complex subunit 10Endoplasmic reticulum
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity ...inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / copper ion transport / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / early endosome / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / 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 8/9 / Uncharacterised protein family (UPF0172) / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / 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, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Carbohydrate-binding-like fold / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6 / Endoplasmic reticulum membrane protein complex subunit 7 / ER membrane protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJanuszyk K / Tomaleri GP / Pleiner T / Voorhees RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137412 United States
CitationJournal: Science / Year: 2020
Title: Structural basis for membrane insertion by the human ER membrane protein complex.
Authors: Tino Pleiner / Giovani Pinton Tomaleri / Kurt Januszyk / Alison J Inglis / Masami Hazu / Rebecca M Voorhees /
Abstract: A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein ...A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved co- and posttranslational insertase at the ER. We determined the structure of the human EMC in a lipid nanodisc to an overall resolution of 3.4 angstroms by cryo-electron microscopy, permitting building of a nearly complete atomic model. We used structure-guided mutagenesis to demonstrate that substrate insertion requires a methionine-rich cytosolic loop and occurs via an enclosed hydrophilic vestibule within the membrane formed by the subunits EMC3 and EMC6. We propose that the EMC uses local membrane thinning and a positively charged patch to decrease the energetic barrier for insertion into the bilayer.
History
DepositionMay 8, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ww7
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21929.png

Downloads & links

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Map

FileDownload / File: emd_21929.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation'Overall' human EMC post-processed, sharpened, and masked map.
Voxel sizeX=Y=Z: 0.836 Å
Density
Contour LevelBy AUTHOR: 0.0035 / Movie #1: 0.0035
Minimum - Maximum-0.019574106 - 0.03154973
Average (Standard dev.)0.00005373367 (±0.00073726283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8360.8360.836
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z267.520267.520267.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0200.0320.000

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Supplemental data

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Mask #1

Fileemd_21929_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human EMC unprocessed, unsharpened, and unmasked 'overall' map.

Fileemd_21929_additional.map
AnnotationHuman EMC unprocessed, unsharpened, and unmasked 'overall' map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 'Overall' human EMC half map

Fileemd_21929_half_map_1.map
Annotation'Overall' human EMC half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 'Overall' human EMC half map

Fileemd_21929_half_map_2.map
Annotation'Overall' human EMC half 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 : Human ER Membrane Protein Complex

EntireName: Human ER Membrane Protein ComplexEndoplasmic reticulum
Components
  • Complex: Human ER Membrane Protein ComplexEndoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 1Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 2Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 3Endoplasmic reticulum
    • Protein or peptide: ER Membrane Protein Complex Subunit 4Endoplasmic reticulum
    • Protein or peptide: Membrane magnesium transporter 1
    • Protein or peptide: ER membrane protein complex subunit 6Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 7Endoplasmic reticulum
    • Protein or peptide: ER membrane protein complex subunit 8Endoplasmic reticulum
  • Protein or peptide: ER membrane protein complex subunit 10Endoplasmic reticulum
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human ER Membrane Protein Complex

SupramoleculeName: Human ER Membrane Protein Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human) / Cell: HEK293

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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: Human (human)
Molecular weightTheoretical: 111.886141 KDa
SequenceString: MAAEWASRFW LWATLLIPAA AVYEDQVGKF DWRQQYVGKV KFASLEFSPG SKKLVVATEK NVIAALNSRT GEILWRHVDK GTAEGAVDA MLLHGQDVIT VSNGGRIMRS WETNIGGLNW EITLDSGSFQ ALGLVGLQES VRYIAVLKKT TLALHHLSSG H LKWVEHLP ...String:
MAAEWASRFW LWATLLIPAA AVYEDQVGKF DWRQQYVGKV KFASLEFSPG SKKLVVATEK NVIAALNSRT GEILWRHVDK GTAEGAVDA MLLHGQDVIT VSNGGRIMRS WETNIGGLNW EITLDSGSFQ ALGLVGLQES VRYIAVLKKT TLALHHLSSG H LKWVEHLP ESDSIHYQMV YSYGSGVVWA LGVVPFSHVN IVKFNVEDGE IVQQVRVSTP WLQHLSGACG VVDEAVLVCP DP SSRSLQT LALETEWELR QIPLQSLDLE FGSGFQPRVL PTQPNPVDAS RAQFFLHLSP SHYALLQYHY GTLSLLKNFP QTA LVSFAT TGEKTVAAVM ACRNEVQKSS SSEDGSMGSF SEKSSSKDSL ACFNQTYTIN LYLVETGRRL LDTTITFSLE QSGT RPERL YIQVFLKKDD SVGYRALVQT EDHLLLFLQQ LAGKVVLWSR EESLAEVVCL EMVDLPLTGA QAELEGEFGK KADGL LGMF LKRLSSQLIL LQAWTSHLWK MFYDARKPRS QIKNEINIDT LARDEFNLQK MMVMVTASGK LFGIESSSGT ILWKQY LPN VKPDSSFKLM VQRTTAHFPH PPQCTLLVKD KESGMSSLYV FNPIFGKWSQ VAPPVLKRPI LQSLLLPVMD QDYAKVL LL IDDEYKVTAF PATRNVLRQL HELAPSIFFY LVDAEQGRLC GYRLRKDLTT ELSWELTIPP EVQRIVKVKG KRSSEHVH S QGRVMGDRSV LYKSLNPNLL AVVTESTDAH HERTFIGIFL IDGVTGRIIH SSVQKKAKGP VHIVHSENWV VYQYWNTKA RRNEFTVLEL YEGTEQYNAT AFSSLDRPQL PQVLQQSYIF PSSISAMEAT ITERGITSRH LLIGLPSGAI LSLPKALLDP RRPEIPTEQ SREENLIPYS PDVQIHAERF INYNQTVSRM RGIYTAPSGL ESTCLVVAYG LDIYQTRVYP SKQFDVLKDD Y DYVLISSV LFGLVFATMI TKRLAQVKLL NRAWR

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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: Human (human)
Molecular weightTheoretical: 34.882531 KDa
SequenceString: MAKVSELYDV TWEEMRDKMR KWREENSRNS EQIVEVGEEL INEYASKLGD DIWIIYEQVM IAALDYGRDD LALFCLQELR RQFPGSHRV KRLTGMRFEA MERYDDAIQL YDRILQEDPT NTAARKRKIA IRKAQGKNVE AIRELNEYLE QFVGDQEAWH E LAELYINE ...String:
MAKVSELYDV TWEEMRDKMR KWREENSRNS EQIVEVGEEL INEYASKLGD DIWIIYEQVM IAALDYGRDD LALFCLQELR RQFPGSHRV KRLTGMRFEA MERYDDAIQL YDRILQEDPT NTAARKRKIA IRKAQGKNVE AIRELNEYLE QFVGDQEAWH E LAELYINE HDYAKAAFCL EELMMTNPHN HLYCQQYAEV KYTQGGLENL ELSRKYFAQA LKLNNRNMRA LFGLYMSASH IA SNPKASA KTKKDNMKYA SWAASQINRA YQFAGRSKKE TKYSLKAVED MLETLQITQS

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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: Human (human)
Molecular weightTheoretical: 29.981924 KDa
SequenceString: MAGPELLLDS NIRLWVVLPI VIITFFVGMI RHYVSILLQS DKKLTQEQVS DSQVLIRSRV LRENGKYIPK QSFLTRKYYF NNPEDGFFK KTKRKVVPPS PMTDPTMLTD MMKGNVTNVL PMILIGGWIN MTFSGFVTTK VPFPLTLRFK PMLQQGIELL T LDASWVSS ...String:
MAGPELLLDS NIRLWVVLPI VIITFFVGMI RHYVSILLQS DKKLTQEQVS DSQVLIRSRV LRENGKYIPK QSFLTRKYYF NNPEDGFFK KTKRKVVPPS PMTDPTMLTD MMKGNVTNVL PMILIGGWIN MTFSGFVTTK VPFPLTLRFK PMLQQGIELL T LDASWVSS ASWYFLNVFG LRSIYSLILG QDNAADQSRM MQEQMTGAAM AMPADTNKAF KTEWEALELT DHQWALDDVE EE LMAKDLH FEGMFKKELQ TSIF

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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: Human (human)
Molecular weightTheoretical: 1.209482 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: Membrane magnesium transporter 1

MacromoleculeName: Membrane magnesium transporter 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.706786 KDa
SequenceString:
MAPSLWKGLV GIGLFALAHA AFSAAQHRSY MRLTEKEDES LPIDIVLQTL LAFAVTCYGI VHIAGEFKDM DATSELKNKT FDTLRNHPS FYVFNHRGRV LFRPSDTANS SNQDALSSNT SLKLRKLESL RR

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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: Human (human)
Molecular weightTheoretical: 12.029248 KDa
SequenceString:
MAAVVAKREG PPFISEAAVR GNAAVLDYCR TSVSALSGAT AGILGLTGLY GFIFYLLASV LLSLLLILKA GRRWNKYFKS RRPLFTGGL IGGLFTYVLF WTFLYGMVHV Y

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Macromolecule #7: ER membrane protein complex subunit 7

MacromoleculeName: ER membrane protein complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 26.501586 KDa
SequenceString: MAAALWGFFP VLLLLLLSGD VQSSEVPGAA AEGSGGSGVG IGDRFKIEGR AVVPGVKPQD WISAARVLVD GEEHVGFLKT DGSFVVHDI PSGSYVVEVV SPAYRFDPVR VDITSKGKMR ARYVNYIKTS EVVRLPYPLQ MKSSGPPSYF IKRESWGWTD F LMNPMVMM ...String:
MAAALWGFFP VLLLLLLSGD VQSSEVPGAA AEGSGGSGVG IGDRFKIEGR AVVPGVKPQD WISAARVLVD GEEHVGFLKT DGSFVVHDI PSGSYVVEVV SPAYRFDPVR VDITSKGKMR ARYVNYIKTS EVVRLPYPLQ MKSSGPPSYF IKRESWGWTD F LMNPMVMM MVLPLLIFVL LPKVVNTSDP DMRREMEQSM NMLNSNHELP DVSEFMTRLF SSKSSGKSSS GSSKTGKSGA GK RR

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Macromolecule #8: ER membrane protein complex subunit 8

MacromoleculeName: ER membrane protein complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 23.807076 KDa
SequenceString: MPGVKLTTQA YCKMVLHGAK YPHCAVNGLL VAEKQKPRKE HLPLGGPGAH HTLFVDCIPL FHGTLALAPM LEVALTLIDS WCKDHSYVI AGYYQANERV KDASPNQVAE KVASRIAEGF SDTALIMVDN TKFTMDCVAP TIHVYEHHEN RWRCRDPHHD Y CEDWPEAQ ...String:
MPGVKLTTQA YCKMVLHGAK YPHCAVNGLL VAEKQKPRKE HLPLGGPGAH HTLFVDCIPL FHGTLALAPM LEVALTLIDS WCKDHSYVI AGYYQANERV KDASPNQVAE KVASRIAEGF SDTALIMVDN TKFTMDCVAP TIHVYEHHEN RWRCRDPHHD Y CEDWPEAQ RISASLLDSR SYETLVDFDN HLDDIRNDWT NPEINKAVLH LC

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Macromolecule #9: ER membrane protein complex subunit 10

MacromoleculeName: ER membrane protein complex subunit 10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 27.375797 KDa
SequenceString: MAAASAGATR LLLLLLMAVA APSRARGSGC RAGTGARGAG AEGREGEACG TVGLLLEHSF EIDDSANFRK RGSLLWNQQD GTLSLSQRQ LSEEERGRLR DVAALNGLYR VRIPRRPGAL DGLEAGGYVS SFVPACSLVE SHLSDQLTLH VDVAGNVVGV S VVTHPGGC ...String:
MAAASAGATR LLLLLLMAVA APSRARGSGC RAGTGARGAG AEGREGEACG TVGLLLEHSF EIDDSANFRK RGSLLWNQQD GTLSLSQRQ LSEEERGRLR DVAALNGLYR VRIPRRPGAL DGLEAGGYVS SFVPACSLVE SHLSDQLTLH VDVAGNVVGV S VVTHPGGC RGHEVEDVDL ELFNTSVQLQ PPTTAPGPET AAFIERLEME QAQKAKNPQE QKSFFAKYWM YIIPVVLFLM MS GAPDTGG QGGGGGGGGG GGSGR

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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: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
50.0 mMHEPES
200.0 mMNaClSodium chloride
2.0 mMMgAc2
1.0 mMDTT
0.05 % (w/v)CHAPSOCHAPS detergent
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K
DetailsSample solubilized and purified in DDM, then reconstituted into lipid nanodisc.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59808 / Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 10 / Number real images: 6345 / Average exposure time: 2.0 sec. / Average electron dose: 59.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1034250
CTF correctionSoftware - Name: cryoSPARC (ver. 2.13.2)
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 188746
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6ww7:
Structure of the human ER membrane protein complex in a lipid nanodisc

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