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- EMDB-35907: cryo-EM structure of human EMC and VDAC -

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Basic information

Entry
Database: EMDB / ID: EMD-35907
Titlecryo-EM structure of human EMC and VDAC
Map data
Sample
  • Complex: EMC_VDAC
    • 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: ER membrane protein complex subunit 5Endoplasmic reticulum
    • 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
    • Protein or peptide: Voltage-dependent anion-selective channel protein 1
KeywordsER membrane protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of calcium import into the mitochondrion / positive regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / voltage-gated monoatomic anion channel activity / omegasome membrane / neuron-neuron synaptic transmission / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Mitochondrial calcium ion transport ...negative regulation of calcium import into the mitochondrion / positive regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / voltage-gated monoatomic anion channel activity / omegasome membrane / neuron-neuron synaptic transmission / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Mitochondrial calcium ion transport / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / ceramide binding / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / regulation of autophagy of mitochondrion / mitochondrial permeability transition pore complex / Pyruvate metabolism / copper ion transport / Mitochondrial protein import / phosphatidylcholine binding / pyruvate metabolic process / oxysterol binding / monoatomic anion transport / cholesterol binding / porin activity / mitochondrial nucleoid / pore complex / autophagosome assembly / RHOA GTPase cycle / negative regulation of reactive oxygen species metabolic process / behavioral fear response / epithelial cell differentiation / PINK1-PRKN Mediated Mitophagy / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / learning / mitochondrial membrane / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / mitochondrial outer membrane / transmembrane transporter binding / early endosome / Ub-specific processing proteases / membrane raft / Golgi membrane / synapse / apoptotic process / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 8/9 / Uncharacterised protein family (UPF0172) / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 / Eukaryotic porin/Tom40 / Eukaryotic porin / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Carbohydrate-binding-like fold / Tetratricopeptide repeat / Porin domain superfamily / 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 / Voltage-dependent anion-selective channel protein 1 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLi M / Zhang C / Wu J / Lei M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930063 China
CitationJournal: Aging (Albany NY) / Year: 2024
Title: Structural insights into human EMC and its interaction with VDAC.
Authors: Mingyue Li / Chunli Zhang / Yuntao Xu / Shaobai Li / Chenhui Huang / Jian Wu / Ming Lei /
Abstract: The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in ...The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
History
DepositionApr 11, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35907.png

Downloads & links

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Map

FileDownload / File: emd_35907.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.52614594 - 1.3342829
Average (Standard dev.)-0.0000015723217 (±0.035136595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 383.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_35907_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_35907_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_35907_half_map_2.map
Projections & Slices
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Sample components

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Entire : EMC_VDAC

EntireName: EMC_VDAC
Components
  • Complex: EMC_VDAC
    • 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: ER membrane protein complex subunit 5Endoplasmic reticulum
    • 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
    • Protein or peptide: Voltage-dependent anion-selective channel protein 1

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Supramolecule #1: EMC_VDAC

SupramoleculeName: EMC_VDAC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (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

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: Homo sapiens (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

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: Homo sapiens (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

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: Homo sapiens (human)
Molecular weightTheoretical: 20.104572 KDa
SequenceString:
MTAQGGLVAN RGRRFKWAIE LSGPGGGSRG RSDRGSGQGD SLYPVGYLDK QVPDTSVQET DRILVEKRCW DIALGPLKQI PMNLFIMYM AGNTISIFPT MMVCMMAWRP IQALMAISAT FKMLESSSQK FLQGLVYLIG NLMGLALAVY KCQSMGLLPT H ASDWLAFI EPPERMEFSG GGLLL

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: Homo sapiens (human)
Molecular weightTheoretical: 14.706786 KDa
SequenceString:
MAPSLWKGLV GIGLFALAHA AFSAAQHRSY MRLTEKEDES LPIDIVLQTL LAFAVTCYGI VHIAGEFKDM DATSELKNKT FDTLRNHPS FYVFNHRGRV LFRPSDTANS SNQDALSSNT SLKLRKLESL RR

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

UniProtKB: ER membrane protein complex subunit 6

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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: Homo sapiens (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

UniProtKB: Endoplasmic reticulum membrane protein complex subunit 7

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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: Homo sapiens (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

UniProtKB: ER membrane protein complex subunit 8

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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: Homo sapiens (human)
Molecular weightTheoretical: 21.781484 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 AAFIERLEM

UniProtKB: ER membrane protein complex subunit 10

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Macromolecule #10: Voltage-dependent anion-selective channel protein 1

MacromoleculeName: Voltage-dependent anion-selective channel protein 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.807521 KDa
SequenceString: MAVPPTYADL GKSARDVFTK GYGFGLIKLD LKTKSENGLE FTSSGSANTE TTKVTGSLET KYRWTEYGLT FTEKWNTDNT LGTEITVED QLARGLKLTF DSSFSPNTGK KNAKIKTGYK REHINLGCDM DFDIAGPSIR GALVLGYEGW LAGYQMNFET A KSRVTQSN ...String:
MAVPPTYADL GKSARDVFTK GYGFGLIKLD LKTKSENGLE FTSSGSANTE TTKVTGSLET KYRWTEYGLT FTEKWNTDNT LGTEITVED QLARGLKLTF DSSFSPNTGK KNAKIKTGYK REHINLGCDM DFDIAGPSIR GALVLGYEGW LAGYQMNFET A KSRVTQSN FAVGYKTDEF QLHTNVNDGT EFGGSIYQKV NKKLETAVNL AWTAGNSNTR FGIAAKYQID PDACFSAKVN NS SLIGLGY TQTLKPGIKL TLSALLDGKN VNAGGHKLGL GLEFQA

UniProtKB: Voltage-dependent anion-selective channel protein 1

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 455504

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