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- PDB-5imy: Trapped Toxin -

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Basic information

Entry
Database: PDB / ID: 5imy
TitleTrapped Toxin
Components
  • CD59 glycoprotein
  • Vaginolysin
Keywordstoxin/toxin receptor / toxin-toxin receptor complex
Function / homology
Function and homology information


negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / host cell membrane / specific granule membrane ...negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / cholesterol binding / tertiary granule membrane / host cell membrane / specific granule membrane / transport vesicle / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / blood coagulation / toxin activity / vesicle / killing of cells of another organism / cell surface receptor signaling pathway / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / : / CD59 glycoprotein / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / : / CD59 glycoprotein / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Vaginolysin / CD59 glycoprotein
Similarity search - Component
Biological speciesGardnerella vaginalis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLawrence, S.L. / Morton, C.J. / Parker, M.W.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Authors: Lawrence, S.L. / Gorman, M.A. / Feil, S.C. / Mulhern, T.D. / Kuiper, M.J. / Ratner, A.J. / Tweten, R.K. / Morton, C.J. / Parker, M.W.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vaginolysin
C: CD59 glycoprotein
D: CD59 glycoprotein
B: Vaginolysin


Theoretical massNumber of molelcules
Total (without water)126,6294
Polymers126,6294
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-17 kcal/mol
Surface area51140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.894, 141.713, 106.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vaginolysin


Mass: 54213.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gardnerella vaginalis (bacteria) / Gene: VLY, vly / Production host: Escherichia coli (E. coli) / References: UniProt: B2YGA4
#2: Protein CD59 glycoprotein / 1F5 antigen / 20 kDa homologous restriction factor / HRF20 / MAC-inhibitory protein / MAC-IP / ...1F5 antigen / 20 kDa homologous restriction factor / HRF20 / MAC-inhibitory protein / MAC-IP / MEM43 antigen / Membrane attack complex inhibition factor / MACIF / Membrane inhibitor of reactive lysis / MIRL / Protectin


Mass: 9101.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD59, MIC11, MIN1, MIN2, MIN3, MSK21 / Production host: Escherichia coli (E. coli) / References: UniProt: P13987
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium acetate, PEG 10000, Bis-Tris, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→48.315 Å / Num. obs: 49244 / % possible obs: 99.9 % / Redundancy: 4.5 % / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3R

1s3r


Resolution: 2.4→42.639 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.71
RfactorNum. reflection% reflection
Rfree0.2759 3128 3.36 %
Rwork0.234 --
obs0.2354 93023 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8653 0 0 137 8790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038869
X-RAY DIFFRACTIONf_angle_d0.71612059
X-RAY DIFFRACTIONf_dihedral_angle_d15.1915341
X-RAY DIFFRACTIONf_chiral_restr0.0451336
X-RAY DIFFRACTIONf_plane_restr0.0041561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43750.37341390.34994103X-RAY DIFFRACTION99
2.4375-2.47750.3971450.33984119X-RAY DIFFRACTION99
2.4775-2.52020.35051400.34074007X-RAY DIFFRACTION99
2.5202-2.5660.37241480.33854156X-RAY DIFFRACTION99
2.566-2.61540.34321400.32284067X-RAY DIFFRACTION99
2.6154-2.66870.35851430.32064117X-RAY DIFFRACTION99
2.6687-2.72680.37951390.3154106X-RAY DIFFRACTION99
2.7268-2.79020.34771410.30514079X-RAY DIFFRACTION100
2.7902-2.85990.35781430.3034095X-RAY DIFFRACTION99
2.8599-2.93720.28211430.29744084X-RAY DIFFRACTION99
2.9372-3.02370.31871450.29474102X-RAY DIFFRACTION100
3.0237-3.12120.34571450.28834093X-RAY DIFFRACTION99
3.1212-3.23270.33021420.2644103X-RAY DIFFRACTION100
3.2327-3.36210.25491450.24714100X-RAY DIFFRACTION99
3.3621-3.51510.29391430.23644074X-RAY DIFFRACTION99
3.5151-3.70030.24261440.22884101X-RAY DIFFRACTION99
3.7003-3.9320.30061420.21794080X-RAY DIFFRACTION99
3.932-4.23530.2631500.19474087X-RAY DIFFRACTION99
4.2353-4.66110.23581360.17484072X-RAY DIFFRACTION98
4.6611-5.33440.2011370.16534017X-RAY DIFFRACTION98
5.3344-6.71660.2271400.20244096X-RAY DIFFRACTION99
6.7166-42.64560.21341380.18424037X-RAY DIFFRACTION98

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