[English] 日本語
Yorodumi
- EMDB-15420: Structure of yeast oligosaccharylransferase complex with lipid-li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15420
TitleStructure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide and non-acceptor peptide bound
Map data
Sample
  • Complex: Yeast OST complex with lipid-linked oligosaccharide and non-acceptor peptide bound
    • Protein or peptide: x 8 types
  • Protein or peptide: x 1 types
  • Ligand: x 6 types
KeywordsN-glycosylation OST complex / TRANSFERASE
Function / homology
Function and homology information


oligosaccharyltransferase I complex / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein glycosylation / endoplasmic reticulum membrane / membrane / 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 / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / dolichyl-diphosphooligosaccharide--protein glycotransferase / OST3 isoform 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 / OST4 isoform 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRamirez AS / de Capitani M / Pesciullesi G / Kowal J / Bloch JS / Irobalieva RN / Aebi M / Reymond JL / Locher KP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase.
Authors: Ana S Ramírez / Mario de Capitani / Giorgio Pesciullesi / Julia Kowal / Joël S Bloch / Rossitza N Irobalieva / Jean-Louis Reymond / Markus Aebi / Kaspar P Locher /
Abstract: Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAcManGlc, from a dolichyl-pyrophosphate donor to ...Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAcManGlc, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites.
History
DepositionJul 19, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_15420.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å
0.85 Å/pix.
x 384 pix.
= 326.4 Å
0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.386
Minimum - Maximum-1.0776811 - 2.1983266
Average (Standard dev.)0.0022371972 (±0.0616464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_15420_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_15420_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Yeast OST complex with lipid-linked oligosaccharide and non-accep...

EntireName: Yeast OST complex with lipid-linked oligosaccharide and non-acceptor peptide bound
Components
  • Complex: Yeast OST complex with lipid-linked oligosaccharide and non-acceptor peptide bound
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycotransferase
    • Protein or peptide: OST4 isoform 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
    • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1
    • Protein or peptide: OST3 isoform 1
  • Protein or peptide: PEPTIDE
  • Ligand: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: MANGANESE (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate

+
Supramolecule #1: Yeast OST complex with lipid-linked oligosaccharide and non-accep...

SupramoleculeName: Yeast OST complex with lipid-linked oligosaccharide and non-acceptor peptide bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 284 KDa

+
Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycotransferase

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycotransferase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 81.604539 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 glycotransferase

+
Macromolecule #2: OST4 isoform 1

MacromoleculeName: OST4 isoform 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.871818 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MISDEQLNSL AITFGIVMMT LIVIYHAVDS TMSPKNRTLQ VDGGSGGSLE VLFQGPTETS QVAPA

UniProtKB: OST4 isoform 1

+
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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 9.52509 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTYEQLYKEF HSSKSFQPFI HLDTQPKFAI CGLIVTLAVL SSALFAVGSK SSYIKKLFFY TILSVIGSLF AGLTTVFASN SFGVYV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.712531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MAKAPKANTP KVTSTSSAVL TDFQETFKTS KRAYFAQIEK YPKLKLIDTF CFFLVLLGVI QCTFIILIRD NFPFNAFLAG FIICVGQFV LLMSLRLQLC NSFPGISKNR AFAEFIVASL ILHFVCLHFI N

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.116477 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.340443 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 FLRSFG

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

+
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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.444438 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

+
Macromolecule #8: OST3 isoform 1

MacromoleculeName: OST3 isoform 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.51816 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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: OST3 isoform 1

+
Macromolecule #9: PEPTIDE

MacromoleculeName: PEPTIDE / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 682.723 Da
SequenceString:
YA(DAB)ATSA

+
Macromolecule #13: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...

MacromoleculeName: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
type: ligand / ID: 13 / Number of copies: 1 / Formula: ELU
Molecular weightTheoretical: 452.459 Da
Chemical component information

ChemComp-ELU:
phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate

+
Macromolecule #14: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 14 / 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

+
Macromolecule #15: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 15 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #16: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
Macromolecule #18: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate

MacromoleculeName: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate
type: ligand / ID: 18 / Number of copies: 1 / Formula: 323
Molecular weightTheoretical: 414.453 Da
Chemical component information

ChemComp-323:
2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75382
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlvh1.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