[English] 日本語
Yorodumi
- EMDB-54064: Structure of the O-oligosaccharyl transferase PglL from Neisseria... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54064
TitleStructure of the O-oligosaccharyl transferase PglL from Neisseria meningitidis in complex with a nanobody
Map dataEM map of NmPglL in complex with a nanobody.
Sample
  • Organelle or cellular component: PglL in complex with a nanobody
    • Protein or peptide: Oligosaccharyltransferase
    • Protein or peptide: Nanobody
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsMembrane protein / glycosyl transferase / O-transferase
Function / homologyVirulence factor membrane-bound polymerase, C-terminal / Virulence factor membrane-bound polymerase, C-terminal / O-antigen ligase-related / : / O-Antigen ligase / protein O-linked glycosylation / transferase activity / membrane / Oligosaccharyltransferase
Function and homology information
Biological speciesNeiserria meningitis (bacteria) / Neisseria meningitidis (bacteria) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHarrison PJ / Naismith JH / Clare DK / Quigley A
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust223727/Z/21/Z United Kingdom
Wellcome Trust02892/Z/16/Z United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: O-oligosaccharyl transferase PglL
Authors: Harrison PJ / Naismith JH / Clare DK / Quigley A
History
DepositionJun 18, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54064.png

Downloads & links

-
Map

FileReleased
AnnotationEM map of NmPglL in complex with a nanobody.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 282 pix.
= 367.164 Å		1.3 Å/pix.
x 282 pix.
= 367.164 Å		1.3 Å/pix.
x 282 pix.
= 367.164 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.47
Minimum - Maximum-4.0303326 - 6.279361
Average (Standard dev.)-0.0015948657 (±0.103216544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282282282
Spacing282282282
CellA=B=C: 367.164 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54064_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of NmPglL in complex with a nanobody.

Fileemd_54064_half_map_1.map
AnnotationHalf map B of NmPglL in complex with a nanobody.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of NmPglL in complex with a nanobody.

Fileemd_54064_half_map_2.map
AnnotationHalf map A of NmPglL in complex with a nanobody.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PglL in complex with a nanobody

EntireName: PglL in complex with a nanobody
Components
  • Organelle or cellular component: PglL in complex with a nanobody
    • Protein or peptide: Oligosaccharyltransferase
    • Protein or peptide: Nanobody
  • Ligand: PHOSPHATIDYLETHANOLAMINE

-
Supramolecule #1: PglL in complex with a nanobody

SupramoleculeName: PglL in complex with a nanobody / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Neiserria meningitis (bacteria)
Molecular weightTheoretical: 83.21964 KDa

-
Macromolecule #1: Oligosaccharyltransferase

MacromoleculeName: Oligosaccharyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 68.008438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAETTVSGA HPAAKLPIYI LPCFLWIGIV PFTFALKLKP SPDFYHDAAA AAGLIVLLFL TAGKKLFDVK IPAISFLLFA MAAFWYLQA RLMNLIYPGM NDIVSWIFIL LAVSAWACRS LVAHFGQERI VTLFAWSLLI GSLLQSCIVV IQFAGWEDTP L FQNIIVYS ...String:
MPAETTVSGA HPAAKLPIYI LPCFLWIGIV PFTFALKLKP SPDFYHDAAA AAGLIVLLFL TAGKKLFDVK IPAISFLLFA MAAFWYLQA RLMNLIYPGM NDIVSWIFIL LAVSAWACRS LVAHFGQERI VTLFAWSLLI GSLLQSCIVV IQFAGWEDTP L FQNIIVYS GQGVIGHIGQ RNNLGHYLMW GILAAAYLNG QRKIPAALGV ICLIMQTAVL GLVNSRTILT YIAAIALILP FW YFRSDKS NRRTMLGIAA AVFLTALFQF SMNTILETFT GIRYETAVER VANGGFTDLP RQIEWNKALA AFQSAPIFGH GWN SFAQQT FLINAEQHNI YDNLLSNLFT HSHNIVLQLL AEMGISGTLL VAATLLTGIA GLLKRPLTPA SLFLICTLAV SMCH SMLEY PLWYVYFLIP FGLMLFLSPA EASDGIAFKK AANLGILTAS AAIFAGLLHL DWTYTRLVNA FSPATDDSAK TLNRK INEL RYISANSPML SFYADFSLVN FALPEYPETQ TWAEEATLKS LKYRPHSATY RIALYLMRQG KVAEAKQWMR ATQSYY PYL MPRYADEIRK LPVWAPLLPE LLKDCKAFAA APGHPEAKPC KENLYFQ

UniProtKB: Oligosaccharyltransferase

-
Macromolecule #2: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.28876 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGRTIR NYGMAWFRQG PGKEREFVAA ISWSGSSTPY ADSVKGRFTI SRDNARNTVY LQLNSLSPE DTAVYYCATD KIYLRASRTP TRDSDYEYWG QGTQVTVSSH HHHHHEPEA

-
Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 256 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse complex of PglL with nanobody purified by gel filtration.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 59547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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