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- EMDB-10110: Cryo-EM structure of human oligosaccharyltransferase complex OST-A -

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Basic information

Entry
Database: EMDB / ID: EMD-10110
TitleCryo-EM structure of human oligosaccharyltransferase complex OST-A
Map data
Sample
  • Complex: Human oligosaccharyltransferase complex OST-A
    • Complex: Human oligosaccharyltransferase complexOligosaccharyltransferase
      • Protein or peptide: x 7 types
    • Complex: Oligosaccharyltransferase complex subunit OSTCOligosaccharyltransferase
      • Protein or peptide: x 1 types
  • Ligand: x 4 types
Function / homology
Function and homology information


oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / co-translational protein modification / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine ...oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / co-translational protein modification / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / protein glycosylation / blastocyst development / Advanced glycosylation endproduct receptor signaling / SRP-dependent cotranslational protein targeting to membrane / enzyme activator activity / rough endoplasmic reticulum / response to endoplasmic reticulum stress / T cell activation / post-translational protein modification / response to cytokine / protein modification process / regulation of protein stability / melanosome / transferase activity / Maturation of spike protein / nuclear body / inflammatory response / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase complex subunit OSTC / Oligosaccharyltransferase 48 kDa subunit beta / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1 / Oligosaccharyltransferase subunit Ribophorin II / Oligosaccaryltransferase ...DAD/Ost2 / Oligosaccharyltransferase complex subunit / DAD family / Oligosaccharyltransferase subunit 5 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit / Oligosaccharyltransferase complex subunit OSTC / 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 48 kDa subunit / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Transmembrane protein 258 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / Oligosaccharyltransferase complex subunit OSTC
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRamirez AS / Kowal J / Locher KP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_147632 Switzerland
CitationJournal: Science / Year: 2019
Title: Cryo-electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B.
Authors: Ana S Ramírez / Julia Kowal / Kaspar P Locher /
Abstract: Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a ...Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) manner. Here, we present high-resolution cryo-electron microscopy structures of human OST-A and OST-B. Although they have similar overall architectures, structural differences in the catalytic subunits STT3A and STT3B facilitate contacts to distinct OST subunits, DC2 in OST-A and MAGT1 in OST-B. In OST-A, interactions with TMEM258 and STT3A allow ribophorin-I to form a four-helix bundle that can bind to a translating ribosome, whereas the equivalent region is disordered in OST-B. We observed an acceptor peptide and dolichylphosphate bound to STT3B, but only dolichylphosphate in STT3A, suggesting distinct affinities of the two OST complexes for protein substrates.
History
DepositionJul 5, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 18, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0106
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0106
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s7o
  • Surface level: 0.0106
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10110.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.0106 / Movie #1: 0.0106
Minimum - Maximum-0.03136922 - 0.05894535
Average (Standard dev.)0.00013422537 (±0.0018610503)
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-0.0310.0590.000

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Supplemental data

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Additional map: Local resolution filtered map from RELION

Fileemd_10110_additional_1.map
AnnotationLocal resolution filtered map from RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_10110_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #2

Fileemd_10110_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : Human oligosaccharyltransferase complex OST-A

EntireName: Human oligosaccharyltransferase complex OST-A
Components
  • Complex: Human oligosaccharyltransferase complex OST-A
    • Complex: Human oligosaccharyltransferase complexOligosaccharyltransferase
      • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
      • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
      • Protein or peptide: Transmembrane protein 258Transmembrane protein
      • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
      • 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 48 kDa subunit
    • Complex: Oligosaccharyltransferase complex subunit OSTCOligosaccharyltransferase
      • Protein or peptide: Oligosaccharyltransferase complex subunit OSTCOligosaccharyltransferase
  • Ligand: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol
  • 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: MAGNESIUM ION
  • Ligand: [(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate

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Supramolecule #1: Human oligosaccharyltransferase complex OST-A

SupramoleculeName: Human oligosaccharyltransferase complex OST-A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: Human oligosaccharyltransferase complex

SupramoleculeName: Human oligosaccharyltransferase complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Oligosaccharyltransferase complex subunit OSTC

SupramoleculeName: Oligosaccharyltransferase complex subunit OSTC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 80.60732 KDa
SequenceString: MTKFGFLRLS YEKQDTLLKL LILSMAAVLS FSTRLFAVLR FESVIHEFDP YFNYRTTRFL AEEGFYKFHN WFDDRAWYPL GRIIGGTIY PGLMITSAAI YHVLHFFHIT IDIRNVCVFL APLFSSFTTI VTYHLTKELK DAGAGLLAAA MIAVVPGYIS R SVAGSYDN ...String:
MTKFGFLRLS YEKQDTLLKL LILSMAAVLS FSTRLFAVLR FESVIHEFDP YFNYRTTRFL AEEGFYKFHN WFDDRAWYPL GRIIGGTIY PGLMITSAAI YHVLHFFHIT IDIRNVCVFL APLFSSFTTI VTYHLTKELK DAGAGLLAAA MIAVVPGYIS R SVAGSYDN EGIAIFCMLL TYYMWIKAVK TGSICWAAKC ALAYFYMVSS WGGYVFLINL IPLHVLVLML TGRFSHRIYV AY CTVYCLG TILSMQISFV GFQPVLSSEH MAAFGVFGLC QIHAFVDYLR SKLNPQQFEV LFRSVISLVG FVLLTVGALL MLT GKISPW TGRFYSLLDP SYAKNNIPII ASVSEHQPTT WSSYYFDLQL LVFMFPVGLY YCFSNLSDAR IFIIMYGVTS MYFS AVMVR LMLVLAPVMC ILSGIGVSQV LSTYMKNLDI SRPDKKSKKQ QDSTYPIKNE VASGMILVMA FFLITYTFHS TWVTS EAYS SPSIVLSARG GDGSRIIFDD FREAYYWLRH NTPEDAKVMS WWDYGYQITA MANRTILVDN NTWNNTHISR VGQAMA STE EKAYEIMREL DVSYVLVIFG GLTGYSSDDI NKFLWMVRIG GSTDTGKHIK ENDYYTPTGE FRVDREGSPV LLNCLMY KM CYYRFGQVYT EAKRPPGFDR VRNAEIGNKD FELDVLEEAY TTEHWLVRIY KVKDLDNRGL SRT

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 4.196004 KDa
SequenceString:
MITDVQLAIF ANMLGVSLFL LVVLYHYVAV NNPKKQE

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Macromolecule #3: Transmembrane protein 258

MacromoleculeName: Transmembrane protein 258 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.083804 KDa
SequenceString:
MELEAMSRYT SPVNPAVFPH LTVVLLAIGM FFTAWFFVYE VTSTKYTRDI YKELLISLVA SLFMGFGVLF LLLWVGIYV

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 12.503631 KDa
SequenceString:
MSASVVSVIS RFLEEYLSST PQRLKLLDAY LLYILLTGAL QFGYCLLVGT FPFNSFLSGF ISCVGSFILA VCLRIQINPQ NKADFQGIS PERAFADFLF ASTILHLVVM NFVG

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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: Human (human)
Molecular weightTheoretical: 68.656156 KDa
SequenceString: MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG GSTSRATSFL LALEPELEAR LAHLGVQVK GEDEEENNLE VRETKIKGKS GRFFTVKLPV ALDPGAKISV IVETVYTHVL HPYPTQITQS EKQFVVFEGN H YFYSPYPT ...String:
MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG GSTSRATSFL LALEPELEAR LAHLGVQVK GEDEEENNLE VRETKIKGKS GRFFTVKLPV ALDPGAKISV IVETVYTHVL HPYPTQITQS EKQFVVFEGN H YFYSPYPT KTQTMRVKLA SRNVESYTKL GNPTRSEDLL DYGPFRDVPA YSQDTFKVHY ENNSPFLTIT SMTRVIEVSH WG NIAVEEN VDLKHTGAVL KGPFSRYDYQ RQPDSGISSI RSFKTILPAA AQDVYYRDEI GNVSTSHLLI LDDSVEMEIR PRF PLFGGW KTHYIVGYNL PSYEYLYNLG DQYALKMRFV DHVFDEQVID SLTVKIILPE GAKNIEIDSP YEISRAPDEL HYTY LDTFG RPVIVAYKKN LVEQHIQDIV VHYTFNKVLM LQEPLLVVAA FYILFFTVII YVRLDFSITK DPAAEARMKV ACITE QVLT LVNKRIGLYR HFDETVNRYK QSRDISTLNS GKKSLETEHK ALTSEIALLQ SRLKTEGSDL CDRVSEMQKL DAQVKE LVL KSAVEAERLV AGKLKKDTYI ENEKLISGKR QELVTKIDHI LDAL

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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: Human (human)
Molecular weightTheoretical: 69.347508 KDa
SequenceString: MAPPGSSTVF LLALTIIAST WALTPTHYLT KHDVERLKAS LDRPFTNLES AFYSIVGLSS LGAQVPDAKK ACTYIRSNLD PSNVDSLFY AAQASQALSG CEISISNETK DLLLAAVSED SSVTQIYHAV AALSGFGLPL ASQEALSALT ARLSKEETVL A TVQALQTA ...String:
MAPPGSSTVF LLALTIIAST WALTPTHYLT KHDVERLKAS LDRPFTNLES AFYSIVGLSS LGAQVPDAKK ACTYIRSNLD PSNVDSLFY AAQASQALSG CEISISNETK DLLLAAVSED SSVTQIYHAV AALSGFGLPL ASQEALSALT ARLSKEETVL A TVQALQTA SHLSQQADLR SIVEEIEDLV ARLDELGGVY LQFEEGLETT ALFVAATYKL MDHVGTEPSI KEDQVIQLMN AI FSKKNFE SLSEAFSVAS AAAVLSHNRY HVPVVVVPEG SASDTHEQAI LRLQVTNVLS QPLTQATVKL EHAKSVASRA TVL QKTSFT PVGDVFELNF MNVKFSSGYY DFLVEVEGDN RYIANTVELR VKISTEVGIT NVDLSTVDKD QSIAPKTTRV TYPA KAKGT FIADSHQNFA LFFQLVDVNT GAELTPHQTF VRLHNQKTGQ EVVFVAEPDN KNVYKFELDT SERKIEFDSA SGTYT LYLI IGDATLKNPI LWNVADVVIK FPEEEAPSTV LSQNLFTPKQ EIQHLFREPE KRPPTVVSNT FTALILSPLL LLFALW IRI GANVSNFTFA PSTIIFHLGH AAMLGLMYVY WTQLNMFQTL KYLAILGSVT FLAGNRMLAQ QAVKRTAH

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Macromolecule #7: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 50.754438 KDa
SequenceString: MGYFRCAGAG SFGRRRKMEP STAARAWALF WLLLPLLGAV CASGPRTLVL LDNLNVRETH SLFFRSLKDR GFELTFKTAD DPSLSLIKY GEFLYDNLII FSPSVEDFGG NINVETISAF IDGGGSVLVA ASSDIGDPLR ELGSECGIEF DEEKTAVIDH H NYDISDLG ...String:
MGYFRCAGAG SFGRRRKMEP STAARAWALF WLLLPLLGAV CASGPRTLVL LDNLNVRETH SLFFRSLKDR GFELTFKTAD DPSLSLIKY GEFLYDNLII FSPSVEDFGG NINVETISAF IDGGGSVLVA ASSDIGDPLR ELGSECGIEF DEEKTAVIDH H NYDISDLG QHTLIVADTE NLLKAPTIVG KSSLNPILFR GVGMVADPDN PLVLDILTGS STSYSFFPDK PITQYPHAVG KN TLLIAGL QARNNARVIF SGSLDFFSDS FFNSAVQKAA PGSQRYSQTG NYELAVALSR WVFKEEGVLR VGPVSHHRVG ETA PPNAYT VTDLVEYSIV IQQLSNGKWV PFDGDDIQLE FVRIDPFVRT FLKKKGGKYS VQFKLPDVYG VFQFKVDYNR LGYT HLYSS TQVSVRPLQH TQYERFIPSA YPYYASAFSM MLGLFIFSIV FLHMKEKEKS D

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Macromolecule #8: Oligosaccharyltransferase complex subunit OSTC

MacromoleculeName: Oligosaccharyltransferase complex subunit OSTC / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.844215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
METLYRVPFL VLECPNLKLK KPPWLHMPSA MTVYALVVVS YFLITGGIIY DVIVEPPSVG SMTDEHGHQR PVAFLAYRVN GQYIMEGLA SSFLFTMGGL GFIILDRSNA PNIPKLNRFL LLFIGFVCVL LSFFMARVFM RMKLPGYLMG

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Macromolecule #12: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R}...

MacromoleculeName: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5- ...Name: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol
type: ligand / ID: 12 / Number of copies: 9 / Formula: KZB
Molecular weightTheoretical: 610.776 Da
Chemical component information

ChemComp-KZB:
(2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol

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Macromolecule #13: (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: 13 / Number of copies: 7 / 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 #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #15: [(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltet...

MacromoleculeName: [(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate
type: ligand / ID: 15 / Number of copies: 1 / Formula: KZE
Molecular weightTheoretical: 508.713 Da
Chemical component information

ChemComp-KZE:
[(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 6035 / Average exposure time: 8.0 sec. / Average electron dose: 68.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 424817
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 156950
FSC plot (resolution estimation)

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