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- EMDB-4161: Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4161
TitleCryo-EM structure of the yeast oligosaccharyltransferase (OST) complex
Map dataNone
Sample
  • Complex: yeast oligosaccharyltransferase (OST) complex
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
KeywordsOST complex / oligosaccharyltransferase / N-linked glycosylation / yeast / MEMBRANE PROTEIN
Function / homology
Function and homology information


Miscellaneous transport and binding events / dolichol-linked oligosaccharide biosynthetic process / protein O-linked glycosylation via mannose / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / : / glycosyltransferase activity ...Miscellaneous transport and binding events / dolichol-linked oligosaccharide biosynthetic process / protein O-linked glycosylation via mannose / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / : / glycosyltransferase activity / protein-disulfide reductase activity / Neutrophil degranulation / post-translational protein modification / nuclear envelope / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / metal ion binding / membrane
Similarity search - Function
: / : / OST48 middle domain / : / Ribophorin_II, C-terminal domain / DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit ...: / : / OST48 middle domain / : / Ribophorin_II, C-terminal domain / DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / OST48, N-terminal domain / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily / Oligosaccaryltransferase / Ribophorin I / Ribophorin I / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / : / STT3/PglB/AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWild R / Kowal J
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationSNF Synergia Transglyco: CRSII3_147632 Switzerland
Swiss National Science FoundationSNF Sinergia GlycoSTART: CRSII5_173709/1 Switzerland
CitationJournal: Science / Year: 2018
Title: Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.
Authors: Rebekka Wild / Julia Kowal / Jillianne Eyring / Elsy M Ngwa / Markus Aebi / Kaspar P Locher /
Abstract: Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to ...Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.
History
DepositionNov 16, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ezn
  • Surface level: 0.037
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4161.png

Downloads & links

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Map

FileDownload / File: emd_4161.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.037
Minimum - Maximum-0.16861129 - 0.29301235
Average (Standard dev.)0.00019375097 (±0.005392874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.500319.500319.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1690.2930.000

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Supplemental data

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Additional map: Map of OST complex in nanodisc, post-processed and masked

Fileemd_4161_additional_1.map
AnnotationMap of OST complex in nanodisc, post-processed and masked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of OST complex, after nanodisc subtraction, post-processed

Fileemd_4161_additional_2.map
AnnotationMap of OST complex, after nanodisc subtraction, post-processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast oligosaccharyltransferase (OST) complex

EntireName: yeast oligosaccharyltransferase (OST) complex
Components
  • Complex: yeast oligosaccharyltransferase (OST) complex
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: yeast oligosaccharyltransferase (OST) complex

SupramoleculeName: yeast oligosaccharyltransferase (OST) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.116477 KDa
SequenceString: MRQVWFSWIV GLFLCFFNVS SAAQYEPPAT WENVDYKRTI DVSNAYISET IEITIKNIAS EPATEYFTAF ESGIFSKVSF FSAYFTNEA TFLNSQLLAN STTAPGDDGE SEIRYGIIQF PNAISPQEEV SLVIKSFYNT VGIPYPEHVG MSEEQHLLWE T NRLPLSAY ...String:
MRQVWFSWIV GLFLCFFNVS SAAQYEPPAT WENVDYKRTI DVSNAYISET IEITIKNIAS EPATEYFTAF ESGIFSKVSF FSAYFTNEA TFLNSQLLAN STTAPGDDGE SEIRYGIIQF PNAISPQEEV SLVIKSFYNT VGIPYPEHVG MSEEQHLLWE T NRLPLSAY DTKKASFTLI GSSSFEEYHP PNDESLLGKA NGNSFEFGPW EDIPRFSSNE TLAIVYSHNA PLNQVVNLRR DI WLSHWAS TIQFEEYYEL TNKAAKLSKG FSRLELMKQI QTQNMRQTHF VTVLDMLLPE GATDHYFTDL VGLVSTSHAE RDH FFIRPR FPIFGGWNYN FTVGWTNKLS DFLHVSSGSD EKFVASIPIL NGPPDTVYDN VELSVFLPEG AEIFDIDSPV PFTN VSIET QKSYFDLNKG HVKLTFSYRN LISQVANGQV LIKYDYPKSS FFKKPLSIAC YIFTALMGVF VLKTLNMNVT N

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1

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Macromolecule #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.712531 KDa
SequenceString:
MAKAPKANTP KVTSTSSAVL TDFQETFKTS KRAYFAQIEK YPKLKLIDTF CFFLVLLGVI QCTFIILIRD NFPFNAFLAG FIICVGQFV LLMSLRLQLC NSFPGISKNR AFAEFIVASL ILHFVCLHFI N

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

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Macromolecule #3: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.51816 KDa
SequenceString: MNWLFLVSLV FFCGVSTHPA LAMSSNRLLK LANKSPKKII PLKDSSFENI LAPPHENAYI VALFTATAPE IGCSLCLELE SEYDTIVAS WFDDHPDAKS SNSDTSIFFT KVNLEDPSKT IPKAFQFFQL NNVPRLFIFK PNSPSILDHS VISISTDTGS E RMKQIIQA ...String:
MNWLFLVSLV FFCGVSTHPA LAMSSNRLLK LANKSPKKII PLKDSSFENI LAPPHENAYI VALFTATAPE IGCSLCLELE SEYDTIVAS WFDDHPDAKS SNSDTSIFFT KVNLEDPSKT IPKAFQFFQL NNVPRLFIFK PNSPSILDHS VISISTDTGS E RMKQIIQA IKQFSQVNDF SLHLPMDWTP IITSTIITFI TVLLFKKQSK LMFSIISSRI IWATLSTFFI ICMISAYMFN QI RNTQLAG VGPKGEVMYF LPNEFQHQFA IETQVMVLIY GTLAALVVVL VKGIQFLRSH LYPETKKAYF IDAILASFCA LFI YVFFAA LTTVFTIKSP AYPFPLLRLS APFK

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3

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Macromolecule #4: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 3.986696 KDa
SequenceString:
MISDEQLNSL AITFGIVMMT LIVIYHAVDS TMSPKN

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4

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Macromolecule #5: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.52509 KDa
SequenceString:
MTYEQLYKEF HSSKSFQPFI HLDTQPKFAI CGLIVTLAVL SSALFAVGSK SSYIKKLFFY TILSVIGSLF AGLTTVFASN SFGVYV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

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Macromolecule #6: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 81.604539 KDa
SequenceString: MGSDRSCVLS VFQTILKLVI FVAIFGAAIS SRLFAVIKFE SIIHEFDPWF NYRATKYLVN NSFYKFLNWF DDRTWYPLGR VTGGTLYPG LMTTSAFIWH ALRNWLGLPI DIRNVCVLFA PLFSGVTAWA TYEFTKEIKD ASAGLLAAGF IAIVPGYISR S VAGSYDNE ...String:
MGSDRSCVLS VFQTILKLVI FVAIFGAAIS SRLFAVIKFE SIIHEFDPWF NYRATKYLVN NSFYKFLNWF DDRTWYPLGR VTGGTLYPG LMTTSAFIWH ALRNWLGLPI DIRNVCVLFA PLFSGVTAWA TYEFTKEIKD ASAGLLAAGF IAIVPGYISR S VAGSYDNE AIAITLLMVT FMFWIKAQKT GSIMHATCAA LFYFYMVSAW GGYVFITNLI PLHVFLLILM GRYSSKLYSA YT TWYAIGT VASMQIPFVG FLPIRSNDHM AALGVFGLIQ IVAFGDFVKG QISTAKFKVI MMVSLFLILV LGVVGLSALT YMG LIAPWT GRFYSLWDTN YAKIHIPIIA SVSEHQPVSW PAFFFDTHFL IWLFPAGVFL LFLDLKDEHV FVIAYSVLCS YFAG VMVRL MLTLTPVICV SAAVALSKIF DIYLDFKTSD RKYAIKPAAL LAKLIVSGSF IFYLYLFVFH STWVTRTAYS SPSVV LPSQ TPDGKLALID DFREAYYWLR MNSDEDSKVA AWWDYGYQIG GMADRTTLVD NNTWNNTHIA IVGKAMASPE EKSYEI LKE HDVDYVLVIF GGLIGFGGDD INKFLWMIRI SEGIWPEEIK ERDFYTAEGE YRVDARASET MRNSLLYKMS YKDFPQL FN GGQATDRVRQ QMITPLDVPP LDYFDEVFTS ENWMVRIYQL KKDDAQGRTL RDVGELTRSS TKTRRSIKRP ELGLRV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3

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Macromolecule #7: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 49.444438 KDa
SequenceString: MRTDWNFFFC ILLQAIFVVG TQTSRTLVLY DQSTEPLEEY SVYLKDLEQR NYKLEYLDIN STSTTVDLYD KEQRLFDNII VFPTKGGKN LARQIPVKQL IKFFENEGNI LCMSSPGAVP NTIRLFLNEL GIYPSPKGHV IRDYFSPSSE ELVVSSNHLL N KYVYNARK ...String:
MRTDWNFFFC ILLQAIFVVG TQTSRTLVLY DQSTEPLEEY SVYLKDLEQR NYKLEYLDIN STSTTVDLYD KEQRLFDNII VFPTKGGKN LARQIPVKQL IKFFENEGNI LCMSSPGAVP NTIRLFLNEL GIYPSPKGHV IRDYFSPSSE ELVVSSNHLL N KYVYNARK SEDFVFGESS AALLENREQI VPILNAPRTS FTESKGKCNS WTSGSQGFLV VGFQNLNNAR LVWIGSSDFL KN KNQDSNQ EFAKELLKWT FNEKSVIKSV HAVHSHADGT SYDEEPYKIK DKVIYSVGFS EWNGEEWLPH IADDIQFELR QVD PYYRLT LSPSGNDSET QYYTTGEFIL PDRHGVFTFL TDYRKIGLSF TTDKDVKAIR HLANDEYPRS WEISNSWVYI SAIC GVIVA WIFFVVSFVT TSSVGKKLET FKKTN

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1

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Macromolecule #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 31.682832 KDa
SequenceString: MQFFKTLAAL VSCISFVLAY VAQDVHVSFP STAGKSRVMI GKVEPRIGID ETVPTTITVE DPNEVIQVNF AIESTNKPFQ NTLLIGLPN KNLEMAFEPE IKDNGKLSMY KYRIDLAKLD AALLQEASRS PEPIKATLIL ASSTAKPKEN LFREILQLNL N FDVDHSDS ...String:
MQFFKTLAAL VSCISFVLAY VAQDVHVSFP STAGKSRVMI GKVEPRIGID ETVPTTITVE DPNEVIQVNF AIESTNKPFQ NTLLIGLPN KNLEMAFEPE IKDNGKLSMY KYRIDLAKLD AALLQEASRS PEPIKATLIL ASSTAKPKEN LFREILQLNL N FDVDHSDS SLVDKFGIKP EIHHIFHAEP KRVAKPIAVI FVLIIFITIL SLIVTWLNSC AAAFNNIPTG VTAVYFLGFI AT IVGFEVI FARYYLGTSI FETLFSSLYL GAPGLLTSTK FLRSFGQTI

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1

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Macromolecule #12: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 12 / Number of copies: 4 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #13: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 13 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, pH 7.5, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and ...Details: Quantifoil carbon grids (300 mesh, copper) were glow discharged at 25 mA for 40 s. 3.5 ul of nanodisc-reconstituted OST sample at concentration of 0.5 mg/ml was applied onto the grid and grids were blotted for 3 s and flash-frozen in a mixture of liquid ethane and propane cooled by liquid nitrogen..
DetailsOST complex reconstituted into nanodisc

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 3915 / Average exposure time: 0.25 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 486361
Startup modelType of model: OTHER / Details: Sphere
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 110091
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6ezn:
Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex

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  • 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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