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- EMDB-7336: The Cryo-EM structure of a eukaryotic oligosaccharyl transferase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7336
TitleThe Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
Map dataEukaryotic oligosaccharyl transferase complex
Sample
  • Complex: oligosaccharyl transferase complex
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
    • 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 SWP1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
  • Ligand: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / TRANSFERASE / glycosylation
Function / homology
Function and homology information


Miscellaneous transport and binding events / dolichol-linked oligosaccharide biosynthetic process / protein O-linked glycosylation via mannose / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / 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 / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / 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: 3.5 Å
AuthorsBai L / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111742 United States
CitationJournal: Nature / Year: 2018
Title: The atomic structure of a eukaryotic oligosaccharyltransferase complex.
Authors: Lin Bai / Tong Wang / Gongpu Zhao / Amanda Kovach / Huilin Li /
Abstract: N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein ...N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein oligosaccharyltransferase (OST) complex that is embedded in the endoplasmic reticulum membrane. Our understanding of eukaryotic protein N-glycosylation has been limited owing to the lack of high-resolution structures. Here we report a 3.5 Å resolution cryo-electron microscopy structure of the Saccharomyces cerevisiae OST complex, revealing the structures of subunits Ost1-Ost5, Stt3, Wbp1 and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interactions with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funnelling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides insights into co-translational protein N-glycosylation, and may facilitate the development of small-molecule inhibitors that target this process.
History
DepositionJan 6, 2018-
Header (metadata) releaseJan 24, 2018-
Map releaseJan 31, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c26
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7336.png

Downloads & links

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Map

FileDownload / File: emd_7336.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEukaryotic oligosaccharyl transferase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.528 Å		1.09 Å/pix.
x 256 pix.
= 278.528 Å		1.09 Å/pix.
x 256 pix.
= 278.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.18846963 - 0.29022458
Average (Standard dev.)0.0008101237 (±0.0073844846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z278.528278.528278.528
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1880.2900.001

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Supplemental data

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Sample components

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Entire : oligosaccharyl transferase complex

EntireName: oligosaccharyl transferase complex
Components
  • Complex: oligosaccharyl transferase complex
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
    • 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 SWP1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
  • Ligand: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: oligosaccharyl transferase complex

SupramoleculeName: oligosaccharyl transferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
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: 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 #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
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: 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 #3: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
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: 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 #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 OST2
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: 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 #6: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3
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: 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 #7: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1
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: 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 #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
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: 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 #11: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)met...

MacromoleculeName: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium
type: ligand / ID: 11 / Number of copies: 8 / Formula: EGY
Molecular weightTheoretical: 636.861 Da
Chemical component information

ChemComp-EGY:
(4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium / phospholipid*YM

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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: 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 823255
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot, UCSF Chimera) / Number images used: 282202
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6c26:
The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex

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