[English] 日本語
Yorodumi
- EMDB-12808: Cryo-EM structure of yeast Ost6p containing oligosaccharyltransfe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12808
TitleCryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex
Map dataLocal resolution filtered map from RELION
Sample
  • Complex: Ost6p containing yeast oligosaccharyltransferase complex
    • Protein or peptide: x 8 types
  • Protein or peptide: x 1 types
  • Ligand: x 5 types
Function / homology
Function and homology information


Miscellaneous transport and binding events / oligosaccharyltransferase I complex / 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 ...Miscellaneous transport and binding events / oligosaccharyltransferase I complex / 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 / protein-macromolecule adaptor activity / nuclear envelope / protein-containing complex assembly / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / metal ion binding
Similarity search - Function
DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase 48 kDa subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccharyltransferase subunit Ribophorin II / Oligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily ...DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase 48 kDa subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccharyltransferase subunit Ribophorin II / 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 SWP1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsWild R / Neuhaus JD / Eyring J / Irobalieva RN / Kowal J / Lin CW / Locher KP / Aebi M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_173709 Switzerland
CitationJournal: Glycobiology / Year: 2021
Title: Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases.
Abstract: The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The ...The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analyzed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.
History
DepositionApr 27, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7oci
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12808.png

Downloads & links

-
Map

FileDownload / File: emd_12808.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map from RELION
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.1587316 - 0.20834993
Average (Standard dev.)7.678363e-06 (±0.0038913386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z322.560322.560322.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1590.2080.000

-
Supplemental data

-
Mask #1

Fileemd_12808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Postprocessed map from RELION

Fileemd_12808_additional_1.map
AnnotationPostprocessed map from RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Gaussian filtered map containing the Ost6p luminal domain

Fileemd_12808_additional_2.map
AnnotationGaussian filtered map containing the Ost6p luminal domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Ost6p containing yeast oligosaccharyltransferase complex

EntireName: Ost6p containing yeast oligosaccharyltransferase complex
Components
  • Complex: Ost6p containing yeast oligosaccharyltransferase complex
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6
    • 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
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1
  • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Digitonin
  • Ligand: MAGNESIUM ION
  • Ligand: Dolichylphosphate

+
Supramolecule #1: Ost6p containing yeast oligosaccharyltransferase complex

SupramoleculeName: Ost6p containing yeast oligosaccharyltransferase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#9
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

+
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 S288C (yeast)
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

+
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 S288C (yeast)
Molecular weightTheoretical: 14.712531 KDa
SequenceString:
MAKAPKANTP KVTSTSSAVL TDFQETFKTS KRAYFAQIEK YPKLKLIDTF CFFLVLLGVI QCTFIILIRD NFPFNAFLAG FIICVGQFV LLMSLRLQLC NSFPGISKNR AFAEFIVASL ILHFVCLHFI N

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 37.921344 KDa
SequenceString: MKWCSTYIII WLAIIFHKFQ KSTATASHNI DDILQLKDDT GVITVTADNY PLLSRGVPGY FNILYITMRG TNSNGMSCQL CHDFEKTYH AVADVIRSQA PQSLNLFFTV DVNEVPQLVK DLKLQNVPHL VVYPPAESNK QSQFEWKTSP FYQYSLVPEN A ENTLQFGD ...String:
MKWCSTYIII WLAIIFHKFQ KSTATASHNI DDILQLKDDT GVITVTADNY PLLSRGVPGY FNILYITMRG TNSNGMSCQL CHDFEKTYH AVADVIRSQA PQSLNLFFTV DVNEVPQLVK DLKLQNVPHL VVYPPAESNK QSQFEWKTSP FYQYSLVPEN A ENTLQFGD FLAKILNISI TVPQAFNVQE FVYYFVACMV VFIFIKKVIL PKVTNKWKLF SMILSLGILL PSITGYKFVE MN AIPFIAR DAKNRIMYFS GGSGWQFGIE IFSVSLMYIV MSALSVLLIY VPKISCVSEK MRGLLSSFLA CVLFYFFSYF ISC YLIKNP GYPIVF

+
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 S288C (yeast)
Molecular weightTheoretical: 3.986696 KDa
SequenceString:
MISDEQLNSL AITFGIVMMT LIVIYHAVDS TMSPKN

+
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 S288C (yeast)
Molecular weightTheoretical: 9.52509 KDa
SequenceString:
MTYEQLYKEF HSSKSFQPFI HLDTQPKFAI CGLIVTLAVL SSALFAVGSK SSYIKKLFFY TILSVIGSLF AGLTTVFASN SFGVYV

+
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 S288C (yeast)
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

+
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 S288C (yeast)
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

+
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 S288C (yeast)
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

+
Macromolecule #9: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM1
type: protein_or_peptide / ID: 9 / Details: alpha-helix modelled as poly-UNK / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
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)

+
Macromolecule #12: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 12 / Number of copies: 6 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

+
Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

+
Macromolecule #14: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 14 / Number of copies: 2 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM / Digitonin

+
Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #16: Dolichylphosphate

MacromoleculeName: Dolichylphosphate / type: ligand / ID: 16 / Number of copies: 1 / Formula: V8K
Molecular weightTheoretical: 847.282 Da
Chemical component information

ChemComp-V8K:
Dolichylphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: RELION
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 220536
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ezn

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7oci:
Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more