[English] 日本語
Yorodumi
- EMDB-17779: Structure of human oligosaccharyltransferase OST-A complex bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17779
TitleStructure of human oligosaccharyltransferase OST-A complex bound to NGI-1
Map data
Sample
  • Complex: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
    • Protein or peptide: x 5 types
  • Protein or peptide: x 3 types
  • Ligand: x 6 types
KeywordsN-glycosylation / OST-A complex / NGI-1 inhibitor / TRANSFERASE
Function / homology
Function and homology information


oligosaccharyltransferase complex binding / : / : / Asparagine N-linked glycosylation / membrane-bounded organelle / oligosaccharyltransferase complex / co-translational protein modification / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine ...oligosaccharyltransferase complex binding / : / : / Asparagine N-linked glycosylation / membrane-bounded organelle / oligosaccharyltransferase complex / co-translational protein modification / 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 / rough endoplasmic reticulum / enzyme activator activity / response to endoplasmic reticulum stress / post-translational protein modification / response to cytokine / T cell activation / protein modification process / regulation of protein stability / melanosome / Maturation of spike protein / nuclear body / inflammatory response / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / 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 ...: / 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 / AglB core domain / 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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsRamirez AS / Kowal J / Locher KP
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_196862 Switzerland
CitationJournal: Cell / Year: 2024
Title: Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-κB.
Authors: Benjamin L Lampson / Ana S Ramίrez / Marta Baro / Lixia He / Mudra Hegde / Vidyasagar Koduri / Jamie L Pfaff / Ruth E Hanna / Julia Kowal / Nitin H Shirole / Yanfeng He / John G Doench / ...Authors: Benjamin L Lampson / Ana S Ramίrez / Marta Baro / Lixia He / Mudra Hegde / Vidyasagar Koduri / Jamie L Pfaff / Ruth E Hanna / Julia Kowal / Nitin H Shirole / Yanfeng He / John G Doench / Joseph N Contessa / Kaspar P Locher / William G Kaelin /
Abstract: Nuclear factor κB (NF-κB) plays roles in various diseases. Many inflammatory signals, such as circulating lipopolysaccharides (LPSs), activate NF-κB via specific receptors. Using whole-genome ...Nuclear factor κB (NF-κB) plays roles in various diseases. Many inflammatory signals, such as circulating lipopolysaccharides (LPSs), activate NF-κB via specific receptors. Using whole-genome CRISPR-Cas9 screens of LPS-treated cells that express an NF-κB-driven suicide gene, we discovered that the LPS receptor Toll-like receptor 4 (TLR4) is specifically dependent on the oligosaccharyltransferase complex OST-A for N-glycosylation and cell-surface localization. The tool compound NGI-1 inhibits OST complexes in vivo, but the underlying molecular mechanism remained unknown. We did a CRISPR base-editor screen for NGI-1-resistant variants of STT3A, the catalytic subunit of OST-A. These variants, in conjunction with cryoelectron microscopy studies, revealed that NGI-1 binds the catalytic site of STT3A, where it traps a molecule of the donor substrate dolichyl-PP-GlcNAc-Man-Glc, suggesting an uncompetitive inhibition mechanism. Our results provide a rationale for and an initial step toward the development of STT3A-specific inhibitors and illustrate the power of contemporaneous base-editor and structural studies to define drug mechanism of action.
History
DepositionJun 30, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17779.png

Downloads & links

-
Map

FileDownload / File: emd_17779.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 331.776 Å		0.65 Å/pix.
x 512 pix.
= 331.776 Å		0.65 Å/pix.
x 512 pix.
= 331.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0735
Minimum - Maximum-0.33379057 - 0.51557744
Average (Standard dev.)0.00034680773 (±0.012341347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 331.776 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_17779_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_17779_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR

EntireName: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
Components
  • Complex: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
    • 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: Oligosaccharyltransferase complex subunit OSTC
  • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
  • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
  • Protein or peptide: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
  • 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: MANGANESE (II) ION
  • Ligand: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
  • Ligand: 5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide
  • Ligand: water

+
Supramolecule #1: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR

SupramoleculeName: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#5, #7
Source (natural)Organism: Homo sapiens (human)

+
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: Homo sapiens (human)
Molecular weightTheoretical: 80.60732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

UniProtKB: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A

+
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
Recombinant expressionOrganism: Homo sapiens (human)
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
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MELEAMSRYT SPVNPAVFPH LTVVLLAIGM FFTAWFFVYE VTSTKYTRDI YKELLISLVA SLFMGFGVLF LLLWVGIYV

UniProtKB: Transmembrane protein 258

+
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
Recombinant expressionOrganism: Homo sapiens (human)
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
Recombinant expressionOrganism: Homo sapiens (human)
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
Recombinant expressionOrganism: Homo sapiens (human)
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: Oligosaccharyltransferase complex subunit OSTC

MacromoleculeName: Oligosaccharyltransferase complex subunit OSTC / type: protein_or_peptide / ID: 7 / 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

UniProtKB: Oligosaccharyltransferase complex subunit OSTC

+
Macromolecule #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...

MacromoleculeName: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.293977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 FLHMKEK

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

+
Macromolecule #13: (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: 13 / Number of copies: 4 / 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 #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: 2 / 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: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

+
Macromolecule #16: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRI...

MacromoleculeName: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
type: ligand / ID: 16 / Number of copies: 1 / Formula: OTP
Molecular weightTheoretical: 722.911 Da
Chemical component information

ChemComp-OTP:
(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE

+
Macromolecule #17: 5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolid...

MacromoleculeName: 5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide
type: ligand / ID: 17 / Number of copies: 1 / Formula: ZXT
Molecular weightTheoretical: 394.512 Da

+
Macromolecule #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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 K3 (6k x 4k) / Average electron dose: 54.2 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:

6s7o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101699
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://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