[English] 日本語
Yorodumi
- EMDB-42441: Major interface of Streptococcal surface enolase dimer from AP53 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42441
TitleMajor interface of Streptococcal surface enolase dimer from AP53 group A streptococcus bound to a lipid vesicle
Map dataMinor interface of streptococcal surface enolase bound to a lipid main map
Sample
  • Complex: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
    • Protein or peptide: Enolase
KeywordsGlycolysis / plasminogen binder / membrane protein / LYASE
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / peptidoglycan-based cell wall / glycolytic process / magnesium ion binding / cell surface / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTjia-Fleck S / Readnour BM / Castellino FJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013423 United States
CitationJournal: To Be Published
Title: Streptococcus surface alpha enolase exposed dimers were found to be the active form on lipid surface that binds to human plasminogen
Authors: Tjia-Fleck S / Readnour BM / Castellino FJ
History
DepositionOct 20, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42441.png

Downloads & links

-
Map

FileDownload / File: emd_42441.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMinor interface of streptococcal surface enolase bound to a lipid main map
Voxel sizeX=Y=Z: 1.078 Å
Density
Contour LevelBy AUTHOR: 0.0578
Minimum - Maximum-2.5252297 - 2.568559
Average (Standard dev.)-0.00012567689 (±0.02503696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 230.69199 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Minor interface of streptococcal surface enolase bound to...

Fileemd_42441_half_map_1.map
AnnotationMinor interface of streptococcal surface enolase bound to a lipid half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Minor interface of streptococcal surface enolase bound to...

Fileemd_42441_half_map_2.map
AnnotationMinor interface of streptococcal surface enolase bound to a lipid half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Streptococcal surface enolase major interface embedded into the s...

EntireName: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
Components
  • Complex: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
    • Protein or peptide: Enolase

-
Supramolecule #1: Streptococcal surface enolase major interface embedded into the s...

SupramoleculeName: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 95 KDa

-
Macromolecule #1: Enolase

MacromoleculeName: Enolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phosphopyruvate hydratase
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 47.543281 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQ AIDRAMIALD GTPNKGKLGA NAILGVSIAV ARAAADYLEV PLYTYLGGFN TKVLPTPMMN IINGGSHSDA P IAFQEFMI ...String:
HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQ AIDRAMIALD GTPNKGKLGA NAILGVSIAV ARAAADYLEV PLYTYLGGFN TKVLPTPMMN IINGGSHSDA P IAFQEFMI MPVGAPTFKE GLRWGAEVFH ALKKILKERG LVTAVGDEGG FAPKFEGTED GVETILKAIE AAGYEAGENG IM IGFDCAS SEFYDKERKV YDYTKFEGEG AAVRTSAEQV DYLEELVNKY PIITIEDGMD ENDWDGWKVL TERLGKRVQL VGD DFFVTN TEYLARGIKE NAANSILIKV NQIGTLTETF EAIEMAKEAG YTAVVSHRSG ETEDSTIADI AVATNAGQIK TGSL SRTDR IAKYNQLLRI EDQLGEVAQY KGIKSFYNLK K

UniProtKB: Enolase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 29.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3300000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ugu

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 7
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 476281
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