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- EMDB-23033: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-23033
TitleCryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent
Map datasharpened map
Sample
  • Complex: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent
    • Complex: endoplasmic reticulum membrane protein complex
      • Protein or peptide: x 9 types
    • Complex: Fab DH4
      • Protein or peptide: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus
Similarity search - Function
Protein Sop4 / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 ...Protein Sop4 / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 1 / ER membrane protein complex subunit 3 / Protein SOP4 / 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 BY4743 (yeast) / Homo sapiens (human) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMiller-Vedam LE / Schirle Oakdale NS / Braeuning B / Boydston EA / Sevillano N / Popova KD / Bonnar JL / Shurtleff MJ / Prabu JR / Stroud RM ...Miller-Vedam LE / Schirle Oakdale NS / Braeuning B / Boydston EA / Sevillano N / Popova KD / Bonnar JL / Shurtleff MJ / Prabu JR / Stroud RM / Craik CS / Schulman BA / Weissman JS / Frost A
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Office of the Director1DP2OD017690-01 United States
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
DepositionNov 24, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ktx
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23033.png

Downloads & links

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Map

FileDownload / File: emd_23033.map.gz / Format: CCP4 / Size: 71.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.06927432 - 0.1280162
Average (Standard dev.)0.0002912958 (±0.003309046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions266266266
Spacing266266266
CellA=B=C: 359.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z266266266
origin x/y/z0.0000.0000.000
length x/y/z359.100359.100359.100
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS266266266
D min/max/mean-0.0690.1280.000

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Supplemental data

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Mask #1

Fileemd_23033_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_23033_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_23033_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_23033_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. cerevisiae endoplasmic reticulum membrane protein complex (EMC...

EntireName: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent
Components
  • Complex: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent
    • Complex: endoplasmic reticulum membrane protein complex
      • 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: Protein SOP4
      • Protein or peptide: Endoplasmic reticulum membrane protein complex subunit 10
      • Protein or peptide: Unassigned helix
    • Complex: Fab DH4
      • Protein or peptide: Fab DH4 heavy chain
      • Protein or peptide: Fab DH4 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC...

SupramoleculeName: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11

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Supramolecule #2: endoplasmic reticulum membrane protein complex

SupramoleculeName: endoplasmic reticulum membrane protein complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8, #11
Source (natural)Organism: Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4741

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Supramolecule #3: Fab DH4

SupramoleculeName: Fab DH4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#10
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant strain: BL21-Gold(DE3)pLysS AG

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 87.272938 KDa
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

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 33.893211 KDa
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

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 28.372842 KDa
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

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 21.478721 KDa
SequenceString:
MSEQEPYEWA KHLLDTKYIE KYNIQNSNTL PSPPGFEGNS SKGNVTRKQQ DATSQTTSLA QKNQITVLQV QKAWQIALQP AKSIPMNIF MSYMSGTSLQ IIPIMTALML LSGPIKAIFS TRSAFKPVLG NKATQSQVQT AMFMYIVFQG VLMYIGYRKL N SMGLIPNA KGDWLPWERI AHYNNGLQWF SD

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 20.489887 KDa
SequenceString:
MSFVSKLLYT VSALVLFHSG FSSYEFHHLL KLNSLNNAQG AISKLPKDIM YETYAGLILF VLAVFTSFEK LQYLPIESND GKIISQGNY LKEIALNKAT NVDNLIGSNP NGEIIFTPSF VDVHMKRKIC REWASNTVKK EKGGSGSGEN LYFQSGSGSD Y KDDDDKDY KDDDDKDYKD DDDK

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 12.411359 KDa
SequenceString:
MSSNEEVFTQ INATANVVDN KKRLLFVQDS SALVLGLVAG FLQIESVHGF IWFLILYNLI NVIYIVWICQ LQPGKFYQSP LHDIFFESF FREITGFVMA WTFGYALIG

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 26.627627 KDa
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

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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: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 22.792824 KDa
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

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Macromolecule #9: Fab DH4 heavy chain

MacromoleculeName: Fab DH4 heavy chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.849994 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAQVQLQQWG AGLLKPSETL SLTCAVYGGS FSGYYWSWIR QPPGKGLEWI GEINHSGSTN YNPSLKSRVT ISVDTSKNQF SLKLSSVTA ADTAVYYCAR GLAGRGYYGS GSYLRWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
MAQVQLQQWG AGLLKPSETL SLTCAVYGGS FSGYYWSWIR QPPGKGLEWI GEINHSGSTN YNPSLKSRVT ISVDTSKNQF SLKLSSVTA ADTAVYYCAR GLAGRGYYGS GSYLRWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC AAAHHHHHHG AA EQKLISE EDLNGAA

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Macromolecule #10: Fab DH4 light chain

MacromoleculeName: Fab DH4 light chain / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.566648 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQTLMNRNG NNFLDWYLQK PGQSPQLLIY LGSNRAPGVP DRFSGSGSG TDFTLRISRV EPEDVGVYYC MQALQTPSFG GGTKVEIRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQTLMNRNG NNFLDWYLQK PGQSPQLLIY LGSNRAPGVP DRFSGSGSG TDFTLRISRV EPEDVGVYYC MQALQTPSFG GGTKVEIRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #11: Unassigned helix

MacromoleculeName: Unassigned helix / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: BY4743
Molecular weightTheoretical: 2.060531 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 6 / 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

BufferpH: 6.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy #1

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Microscopy ID1
DetailsDataset 1 collected on FEI Polara at UCSF on August 22nd, 2016.
Image recordingImage recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.8 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Electron microscopy #1~

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Microscopy ID1
DetailsDataset 2 collected on FEI Titan Krios at Janelia Research Campus on October 20th, 2016.
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 58.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: These two datasets were processed independently initially. Upon selecting the best subset of data and then re-extracted and scaled to the same pixel size and combined to get to the final 4.3 ...Details: These two datasets were processed independently initially. Upon selecting the best subset of data and then re-extracted and scaled to the same pixel size and combined to get to the final 4.3 A resolution maps and model.
Number images used: 83599
Image processing ID1
Image recording ID1
FSC plot (resolution estimation)

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Image processing #2

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170186
Image processing ID2
Image recording ID2
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7ktx:
Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent

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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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