[English] 日本語
Yorodumi
- EMDB-10112: Cryo-EM structure of human oligosaccharyltransferase complex OST-B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10112
TitleCryo-EM structure of human oligosaccharyltransferase complex OST-B
Map data
Sample
  • Complex: Human oligosaccharyltransferase complex OST-B
    • Complex: Human oligosaccharyltransferase complex
      • Protein or peptide: x 9 types
    • Complex: Magnesium transporter protein 1
      • Protein or peptide: x 1 types
  • Ligand: x 4 types
KeywordsN-glycosylation / Oligosaccharyltransferase / OSTB / TRANSFERASE
Function / homology
Function and homology information


oligosaccharyltransferase complex binding / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / Asparagine N-linked glycosylation / magnesium ion transport / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / Miscellaneous transport and binding events / glycoprotein catabolic process ...oligosaccharyltransferase complex binding / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / Asparagine N-linked glycosylation / magnesium ion transport / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / oligosaccharyltransferase complex / Miscellaneous transport and binding events / glycoprotein catabolic process / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / : / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / : / Advanced glycosylation endproduct receptor signaling / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / response to unfolded protein / specific granule membrane / rough endoplasmic reticulum / ERAD pathway / response to cytokine / post-translational protein modification / response to endoplasmic reticulum stress / T cell activation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / enzyme activator activity / regulation of protein stability / protein modification process / transmembrane transport / cognition / melanosome / transferase activity / carbohydrate binding / Maturation of spike protein / nuclear body / inflammatory response / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Malectin / : / : / : / Ribophorin II third domain / Ribophorin II second domain / Ribophorin II N-terminal domain / : / : ...: / Malectin / : / : / : / Ribophorin II third domain / Ribophorin II second domain / Ribophorin II N-terminal domain / : / : / OST48 middle domain / : / Ribophorin_II, C-terminal domain / DAD/Ost2 / Oligosaccharyltransferase complex subunit / Malectin domain / DAD family / Oligosaccharyltransferase subunit 5 / Malectin domain / 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 / Thioredoxin-like superfamily
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 TMEM258 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 / Malectin / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit MAGT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRamirez AS / Kowal J
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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6s7t
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10112.png

Downloads & links

-
Map

FileDownload / File: emd_10112.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.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.05921699 - 0.08478952
Average (Standard dev.)-0.000011908643 (±0.002091532)
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-0.0590.085-0.000

-
Supplemental data

-
Additional map: Local resolution filtered map from RELION

Fileemd_10112_additional_1.map
AnnotationLocal resolution filtered map from RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_10112_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Human oligosaccharyltransferase complex OST-B

EntireName: Human oligosaccharyltransferase complex OST-B
Components
  • Complex: Human oligosaccharyltransferase complex OST-B
    • Complex: Human oligosaccharyltransferase complex
      • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B
      • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
      • Protein or peptide: Transmembrane protein 258
      • 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
      • Protein or peptide: Malectin
      • Protein or peptide: PEPTIDE
    • Complex: Magnesium transporter protein 1
      • Protein or peptide: Magnesium transporter protein 1
  • 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~{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: MAGNESIUM ION
  • Ligand: (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate

+
Supramolecule #1: Human oligosaccharyltransferase complex OST-B

SupramoleculeName: Human oligosaccharyltransferase complex OST-B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10

+
Supramolecule #2: Human oligosaccharyltransferase complex

SupramoleculeName: Human oligosaccharyltransferase complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #9-#10
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Magnesium transporter protein 1

SupramoleculeName: Magnesium transporter protein 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-diphosphooligosaccharide-protein glycotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.781047 KDa
SequenceString: MAEPSAPESK HKSSLNSSPW SGLMALGNSR HGHHGPGAQC AHKAAGGAAP PKPAPAGLSG GLSQPAGWQS LLSFTILFLA WLAGFSSRL FAVIRFESII HEFDPWFNYR STHHLASHGF YEFLNWFDER AWYPLGRIVG GTVYPGLMIT AGLIHWILNT L NITVHIRD ...String:
MAEPSAPESK HKSSLNSSPW SGLMALGNSR HGHHGPGAQC AHKAAGGAAP PKPAPAGLSG GLSQPAGWQS LLSFTILFLA WLAGFSSRL FAVIRFESII HEFDPWFNYR STHHLASHGF YEFLNWFDER AWYPLGRIVG GTVYPGLMIT AGLIHWILNT L NITVHIRD VCVFLAPTFS GLTSISTFLL TRELWNQGAG LLAACFIAIV PGYISRSVAG SFDNEGIAIF ALQFTYYLWV KS VKTGSVF WTMCCCLSYF YMVSAWGGYV FIINLIPLHV FVLLLMQRYS KRVYIAYSTF YIVGLILSMQ IPFVGFQPIR TSE HMAAAG VFALLQAYAF LQYLRDRLTK QEFQTLFFLG VSLAAGAVFL SVIYLTYTGY IAPWSGRFYS LWDTGYAKIH IPII ASVSE HQPTTWVSFF FDLHILVCTF PAGLWFCIKN INDERVFVAL YAISAVYFAG VMVRLMLTLT PVVCMLSAIA FSNVF EHYL GDDMKRENPP VEDSSDEDDK RNQGNLYDKA GKVRKHATEQ EKTEEGLGPN IKSIVTMLML MLLMMFAVHC TWVTSN AYS SPSVVLASYN HDGTRNILDD FREAYFWLRQ NTDEHARVMS WWDYGYQIAG MANRTTLVDN NTWNNSHIAL VGKAMSS NE TAAYKIMRTL DVDYVLVIFG GVIGYSGDDI NKFLWMVRIA EGEHPKDIRE SDYFTPQGEF RVDKAGSPTL LNCLMYKM S YYRFGEMQLD FRTPPGFDRT RNAEIGNKDI KFKHLEEAFT SEHWLVRIYK VKAPDNRETL DHKPRVTNIF PKQKYLSKK TTKRKRGYIK NKLVFKKGKK ISKKTV

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B

+
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: Homo sapiens (human)
Molecular weightTheoretical: 4.196004 KDa
SequenceString:
MITDVQLAIF ANMLGVSLFL LVVLYHYVAV NNPKKQE

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4

+
Macromolecule #3: Transmembrane protein 258

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

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258

+
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: Homo sapiens (human)
Molecular weightTheoretical: 12.503631 KDa
SequenceString:
MSASVVSVIS RFLEEYLSST PQRLKLLDAY LLYILLTGAL QFGYCLLVGT FPFNSFLSGF ISCVGSFILA VCLRIQINPQ NKADFQGIS PERAFADFLF ASTILHLVVM NFVG

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

+
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: Homo sapiens (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

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: Homo sapiens (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

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

+
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: Homo sapiens (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

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

+
Macromolecule #8: Magnesium transporter protein 1

MacromoleculeName: Magnesium transporter protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.08157 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAARWRFWCV SVTMVVALLI VCDVPSASAQ RKKEMVLSEK VSQLMEWTNK RPVIRMNGDK FRRLVKAPPR NYSVIVMFTA LQLHRQCVV CKQADEEFQI LANSWRYSSA FTNRIFFAMV DFDEGSDVFQ MLNMNSAPTF INFPAKGKPK RGDTYELQVR G FSAEQIAR ...String:
MAARWRFWCV SVTMVVALLI VCDVPSASAQ RKKEMVLSEK VSQLMEWTNK RPVIRMNGDK FRRLVKAPPR NYSVIVMFTA LQLHRQCVV CKQADEEFQI LANSWRYSSA FTNRIFFAMV DFDEGSDVFQ MLNMNSAPTF INFPAKGKPK RGDTYELQVR G FSAEQIAR WIADRTDVNI RVIRPPNYAG PLMLGLLLAV IGGLVYLRRS NMEFLFNKTG WAFAALCFVL AMTSGQMWNH IR GPPYAHK NPHTGHVNYI HGSSQAQFVA ETHIVLLFNG GVTLGMVLLC EAATSDMDIG KRKIMCVAGI GLVVLFFSWM LSI FRSKYH GYPYSFLMS

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit MAGT1

+
Macromolecule #9: Malectin

MacromoleculeName: Malectin / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.270779 KDa
SequenceString: MLGAWAVEGT AVALLRLLLL LLPPAIRGPG LGVAGVAGAA GAGLPESVIW AVNAGGEAHV DVHGIHFRKD PLEGRVGRAS DYGMKLPIL RSNPEDQILY QTERYNEETF GYEVPIKEEG DYVLVLKFAE VYFAQSQQKV FDVRLNGHVV VKDLDIFDRV G HSTAHDEI ...String:
MLGAWAVEGT AVALLRLLLL LLPPAIRGPG LGVAGVAGAA GAGLPESVIW AVNAGGEAHV DVHGIHFRKD PLEGRVGRAS DYGMKLPIL RSNPEDQILY QTERYNEETF GYEVPIKEEG DYVLVLKFAE VYFAQSQQKV FDVRLNGHVV VKDLDIFDRV G HSTAHDEI IPMSIRKGKL SVQGEVSTFT GKLYIEFVKG YYDNPKVCAL YIMAGTVDDV PKLQPHPGLE KKEEEEEEEE YD EGSNLKK QTNKNRVQSG PRTPNPYASD NSSLMFPILV AFGVFIPTLF CLCRL

UniProtKB: Malectin

+
Macromolecule #10: PEPTIDE

MacromoleculeName: PEPTIDE / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 588.611 Da
SequenceString:
AANATAA

+
Macromolecule #14: (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: 14 / Number of copies: 10 / 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

+
Macromolecule #15: (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: 15 / Number of copies: 13 / 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

+
Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #17: (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotri...

MacromoleculeName: (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate
type: ligand / ID: 17 / Number of copies: 1 / Formula: 0K3
Molecular weightTheoretical: 642.931 Da
Chemical component information

ChemComp-0K3:
(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate

-
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
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 14705 / Average exposure time: 8.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

+
Image processing

Particle selectionNumber selected: 1106821
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: RELION (ver. 3.0) / Number images used: 249725
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

+
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