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- EMDB-11732: Cryo-EM structure of human ER membrane protein complex in lipid n... -

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Basic information

Entry
Database: EMDB / ID: EMD-11732
TitleCryo-EM structure of human ER membrane protein complex in lipid nanodiscs
Map dataConsensus map of hEMC in nanodiscs
Sample
  • Complex: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
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 / apoptotic process / 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) / 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 ...ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / 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 / 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 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: 3.39 Å
AuthorsBraeuning B / Prabu JR / Miller-Vedam LE / Weissman JS / Frost A / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Max Planck Society Germany
CitationJournal: Elife / Year: 2020
Title: Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients.
Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J ...Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J Shurtleff / Robert M Stroud / Charles S Craik / Brenda A Schulman / Adam Frost / Jonathan S Weissman /
Abstract: Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player ...Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
History
DepositionSep 15, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.36
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ado
  • Surface level: 0.36
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11732.png

Downloads & links

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Map

FileDownload / File: emd_11732.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of hEMC in nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 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: 0.36 / Movie #1: 0.36
Minimum - Maximum-1.1078776 - 2.3187323
Average (Standard dev.)-0.00031519795 (±0.054983426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85120.85120.8512
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z340.480340.480340.480
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.1082.319-0.000

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Supplemental data

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Mask #1

Fileemd_11732_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused cytoplasm map of hEMC in nanodiscs

Fileemd_11732_additional_1.map
AnnotationFocused cytoplasm map of hEMC in nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused lumen map of hEMC in nanodiscs

Fileemd_11732_additional_2.map
AnnotationFocused lumen map of hEMC in nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sidesplitter map of hEMC in nanodiscs

Fileemd_11732_additional_3.map
AnnotationSidesplitter map of hEMC in nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus map of hEMC in nanodiscs - subclassified...

Fileemd_11732_additional_4.map
AnnotationConsensus map of hEMC in nanodiscs - subclassified on EMC7 lumenal domain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map of hEMC in nanodiscs - Halfmap 1

Fileemd_11732_half_map_1.map
AnnotationConsensus map of hEMC in nanodiscs - Halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map of hEMC in nanodiscs - Halfmap 2

Fileemd_11732_half_map_2.map
AnnotationConsensus map of hEMC in nanodiscs - Halfmap 2
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 endoplasmic reticulum membrane protein complex (EMC) in POP...

EntireName: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs
Components
  • Complex: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs
    • 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
    • Protein or peptide: Unassigned helix
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Human endoplasmic reticulum membrane protein complex (EMC) in POP...

SupramoleculeName: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293 GnTI- / Recombinant plasmid: pEG
Molecular weightTheoretical: 300 KDa

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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
Recombinant expressionOrganism: Homo sapiens (human)
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: Homo sapiens (human)
Molecular weightTheoretical: 34.882531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: Homo sapiens (human)
Molecular weightTheoretical: 29.981924 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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
Details: There is no mutations but sequence from model and input are not aligning well.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.104572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MTAQGGLVAN RGRRFKWAIE LSGPGGGSRG RSDRGSGQGD SLYPVGYLDK QVPDTSVQET DRILVEKRCW DIALGPLKQI PMNLFIMYM AGNTISIFPT MMVCMMAWRP IQALMAISAT FKMLESSSQK FLQGLVYLIG NLMGLALAVY KCQSMGLLPT H ASDWLAFI EPPERMEFSG GGLLL

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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: Homo sapiens (human)
Molecular weightTheoretical: 15.703762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAPSLWKGLV GIGLFALAHA AFSAAQHRSY MRLTEKEDES LPIDIVLQTL LAFAVTCYGI VHIAGEFKDM DATSELKNKT FDTLRNHPS FYVFNHRGRV LFRPSDTANS SNQDALSSNT SLKLRKLESL RRDYKDDDDK

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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
Recombinant expressionOrganism: Homo sapiens (human)
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: Homo sapiens (human)
Molecular weightTheoretical: 26.501586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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
Details: Map modelled as EMC8; both EMC8 and its paralog EMC9 (44% identity) were co-expressed and turns out they can both occupy same position on complex in mutually exclusive manner. We chose to ...Details: Map modelled as EMC8; both EMC8 and its paralog EMC9 (44% identity) were co-expressed and turns out they can both occupy same position on complex in mutually exclusive manner. We chose to model as EMC8 but note that map is likely superposition of both.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.807076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: Homo sapiens (human)
Molecular weightTheoretical: 27.446875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAASAGAT RLLLLLLMAV AAPSRARGSG CRAGTGARGA GAEGREGEAC GTVGLLLEHS FEIDDSANFR KRGSLLWNQQ DGTLSLSQR QLSEEERGRL RDVAALNGLY RVRIPRRPGA LDGLEAGGYV SSFVPACSLV ESHLSDQLTL HVDVAGNVVG V SVVTHPGG ...String:
MAAAASAGAT RLLLLLLMAV AAPSRARGSG CRAGTGARGA GAEGREGEAC GTVGLLLEHS FEIDDSANFR KRGSLLWNQQ DGTLSLSQR QLSEEERGRL RDVAALNGLY RVRIPRRPGA LDGLEAGGYV SSFVPACSLV ESHLSDQLTL HVDVAGNVVG V SVVTHPGG CRGHEVEDVD LELFNTSVQL QPPTTAPGPE TAAFIERLEM EQAQKAKNPQ EQKSFFAKYW MYIIPVVLFL MM SGAPDTG GQGGGGGGGG GGGSGR

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Macromolecule #10: Unassigned helix

MacromoleculeName: Unassigned helix / type: protein_or_peptide / ID: 10
Details: This is transmembrane alpha-helix which was modeled as poly-alanine.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.379692 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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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: 4 / 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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Macromolecule #12: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 5 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*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

Concentration2 mg/mL
BufferpH: 6
Details: 10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 72.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 177560
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7ado:
Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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