[English] 日本語
Yorodumi
- EMDB-36688: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36688
Titlealpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
Map dataB-factor Sharpened map with B-factor value of -60
Sample
  • Complex: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag
    • Protein or peptide: alpha hemolysin fused with spy-catcher
    • Protein or peptide: alpha hemolysin fused with spy-tag
Keywordspore / chimera protein / spy-catcher / spy-tag / dimer / TOXIN
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsIshii Y / Naito K / Yokoyama T / Tanaka Y / Matsuura T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
Authors: Ishii Y / Naito K / Yokoyama T / Tanaka Y / Matsuura T
History
DepositionJun 30, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36688.png

Downloads & links

-
Map

FileDownload / File: emd_36688.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor Sharpened map with B-factor value of -60
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.9747703 - 2.1897957
Average (Standard dev.)0.004037175 (±0.06506082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 315.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: one of the half maps

Fileemd_36688_half_map_1.map
Annotationone of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: one of the half maps

Fileemd_36688_half_map_2.map
Annotationone of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag

EntireName: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag
Components
  • Complex: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag
    • Protein or peptide: alpha hemolysin fused with spy-catcher
    • Protein or peptide: alpha hemolysin fused with spy-tag

-
Supramolecule #1: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag

SupramoleculeName: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

-
Macromolecule #1: alpha hemolysin fused with spy-catcher

MacromoleculeName: alpha hemolysin fused with spy-catcher / type: protein_or_peptide / ID: 1 / Details: 300-412:SpyCatcher / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 47.003504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String:
MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRK AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSVTTLSGLS GEQGPSGDMT TEE DSATHI KFSKRDEDGR ELAGATMELR DSSGKTISTW ISDGHVKDFY LYPGKYTFVE TAAPDGYEVA TPIEFTVNED GQVT VDGEA TEGDAHTGGS HHHHHH

UniProtKB: Alpha-hemolysin

-
Macromolecule #2: alpha hemolysin fused with spy-tag

MacromoleculeName: alpha hemolysin fused with spy-tag / type: protein_or_peptide / ID: 2 / Details: 300-315:SpyTag / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 36.803934 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String:
MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRK AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSRGVPHIVM VDAYKRYKGG SHH HHHH

UniProtKB: Alpha-hemolysin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.58 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
20.0 mMHEPES-KOH
50.0 mMPotassium glutamate

Details: 20mM HEPES-KOH[pH7.6], 50mM Potassium glutamate
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
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