[English] 日本語
Yorodumi
- PDB-8jbq: Pro-alpha-hemolysin of Vibrio campbellii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jbq
TitlePro-alpha-hemolysin of Vibrio campbellii
ComponentsHemolysin
KeywordsTOXIN / Hemolysin / Pore forming toxin
Function / homology:
Function and homology information
Biological speciesVibrio campbellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, S.M. / Chen, Y.A. / Chiu, Y.C.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 109-2636-B-006 -012 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 110-2636-B-006 -012 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 111-2636-B-006 -012 Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for calcium-stimulating pore formation of Vibrio α-hemolysin.
Authors: Yu-Chuan Chiu / Min-Chi Yeh / Chun-Hsiung Wang / Yu-An Chen / Hsiang Chang / Han-You Lin / Meng-Chiao Ho / Shih-Ming Lin /
Abstract: Vibrio α-hemolysins (αHLs) are β-pore-forming toxins secreted by Vibrio pathogens, crucial for the facilitation of bacterial infections through host cell lysis. These toxins are produced as ...Vibrio α-hemolysins (αHLs) are β-pore-forming toxins secreted by Vibrio pathogens, crucial for the facilitation of bacterial infections through host cell lysis. These toxins are produced as inactive precursors, requiring proteolytic maturation and membrane association for activation within host tissues. Here, we investigate Vibrio campbellii αHL (VcαHL), and establish that its hemolytic activity is significantly stimulated by calcium ions, with an EC that aligns with physiological calcium concentrations. Furthermore, we illustrate the vital contribution of calcium ions to the oligomerization of VcαHL on membranes. Using X-ray crystallography and cryo-electron microscopy, we decipher both the immature and assembled structures of VcαHL and elucidate the conformational changes corresponding to toxin assembly. We also identify a calcium-binding module that is integral for VcαHL's calcium-dependent activation. These findings provide insights into the regulatory mechanisms of VcαHL and have the potential to inform the development of targeted therapeutic strategies against Vibrio infections.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9324
Polymers80,6441
Non-polymers2883
Water11,169620
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.825, 208.825, 52.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1260-

HOH

21A-1431-

HOH

-
Components

#1: Protein Hemolysin / alpha-Hemolysin


Mass: 80643.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio campbellii (bacteria) / Gene: DSB67_23490 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta-gami 2 / References: UniProt: A0A344KRS4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM sodium cacodylate/HCl, 200 mM lithium sulfate, and 30% (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 78663 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 29.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 16.18
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 7754 / CC1/2: 0.727 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 1997 2.54 %
Rwork0.1802 76481 -
obs0.1807 78478 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5435 0 15 620 6070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195609
X-RAY DIFFRACTIONf_angle_d0.47387634
X-RAY DIFFRACTIONf_chiral_restr0.0422828
X-RAY DIFFRACTIONf_plane_restr0.00311012
X-RAY DIFFRACTIONf_dihedral_angle_d18.8989772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24231410.24235387X-RAY DIFFRACTION99.8
2.05-2.110.28111400.22785386X-RAY DIFFRACTION99.69
2.11-2.170.23851400.22465350X-RAY DIFFRACTION99.76
2.17-2.240.21441400.20585374X-RAY DIFFRACTION99.71
2.24-2.320.23981410.20345399X-RAY DIFFRACTION99.8
2.32-2.410.23521420.19795395X-RAY DIFFRACTION99.84
2.41-2.520.2111400.1985415X-RAY DIFFRACTION99.93
2.52-2.650.24321430.20275451X-RAY DIFFRACTION100
2.65-2.820.20751420.1915435X-RAY DIFFRACTION100
2.82-3.040.20411430.19095480X-RAY DIFFRACTION100
3.04-3.340.19251430.17635473X-RAY DIFFRACTION100
3.34-3.820.1881440.1645521X-RAY DIFFRACTION100
3.82-4.810.14321450.13925590X-RAY DIFFRACTION99.95
4.81-29.550.18281530.17435825X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.63873108875-2.5008811051.197140690032.73020311763-0.5937161384175.212174101410.1305426188030.458849660384-0.17270336403-0.334780748604-0.06928739408060.1994771527130.434332187836-0.265606537233-0.03685583053940.357477827298-0.019418631470.00361198104160.241459458941-0.01770322399750.186700937907-72.163828718325.1938164299-21.0227357952
20.267429780753-0.21550712183-0.08565959147742.40947117070.9163857448630.8899897475980.0284432894920.0004096725482110.007462119785240.144770803951-0.0375336783272-0.001405301781770.1780673660830.04424981272640.01251148845810.154950171912-0.01267833939580.01081088459990.150748864350.007386029455930.131427679768-69.842087246835.98520357217.8481941167
32.649575508130.50759589742-0.0536747821694.117907847730.9747875649661.99296921273-0.00938017001041-0.01948947621310.119652426170.02302681722180.00341158810306-0.0783420772345-0.1146183883610.01850561325250.006989374214070.3319195569940.0689976439665-0.002787273908350.157954885215-0.007608035182950.172011217271-60.4095985955-3.69968504295-16.6655458194
41.498699631880.586608962665-0.8638500497893.680323656121.9887656732.27265056370.120919766379-0.1511135201050.77759319921-0.1225129926970.2655732791-0.95533234584-0.4453303999030.184479105341-0.324721946680.4595214633080.0222534733065-0.007066544332420.354408146823-0.1142085197830.840063840946-37.7981559451.3994153536-16.829508019
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 92 )0 - 921 - 93
22chain 'A' and (resid 93 through 452 )93 - 45294 - 431
33chain 'A' and (resid 453 through 602 )453 - 602432 - 581
44chain 'A' and (resid 603 through 713 )603 - 713582 - 692

+
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