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- PDB-4tsy: Crystal structure of FraC with lipids -

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Basic information

Entry
Database: PDB / ID: 4tsy
TitleCrystal structure of FraC with lipids
ComponentsFragaceatoxin C
KeywordsTOXIN / actinoporin pore-forming toxin / Membrane lipids / Phosphocholine / Lipid-protein interaction
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
HEPTANE-1,2,3-TRIOL / Chem-HXJ / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsCaaveiro, J.M.M. / Tanaka, K. / Tsumoto, K.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Gonzalez-Manas, J.M. / Tsumoto, K.
#1: Journal: Toxicon / Year: 2009
Title: Purification, cloning and characterization of fragaceatoxin C, a novel actinoporin from the sea anemone Actinia fragacea
Authors: Bellomio, A. / Morante, K. / Barlic, A. / Gutierrez-Aguirre, I. / Viguera, A.R. / Gonzalez-Manas, J.M.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fragaceatoxin C
B: Fragaceatoxin C
C: Fragaceatoxin C
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,37736
Polymers78,9854
Non-polymers7,39232
Water30617
1
A: Fragaceatoxin C
B: Fragaceatoxin C
C: Fragaceatoxin C
D: Fragaceatoxin C
hetero molecules

A: Fragaceatoxin C
B: Fragaceatoxin C
C: Fragaceatoxin C
D: Fragaceatoxin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,75572
Polymers157,9708
Non-polymers14,78464
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_355-x-2,y,-z+1/21
Buried area23450 Å2
ΔGint-623 kcal/mol
Surface area61220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.337, 199.879, 120.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 4 - 179 / Label seq-ID: 4 - 179

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Fragaceatoxin C / fraC


Mass: 19746.303 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Plasmid: pGEM-T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9W5G6
#2: Chemical
ChemComp-HXJ / 2-[[(E,2S,3R)-2-(hexanoylamino)-3-oxidanyl-dec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium


Mass: 451.558 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H44N2O6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 77.07 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: Jeffamine M600, 1,2,3-heptanetriol, monoolein, ammonium sulfate, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→38.65 Å / Num. obs: 30154 / % possible obs: 94.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.9
Reflection shellResolution: 3.14→3.32 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / % possible all: 83.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 3.14→38.65 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / SU B: 33.743 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.732 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22123 1526 5.1 %RANDOM
Rwork0.19852 ---
obs0.19967 28628 93.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--2.83 Å20 Å2
3----2.73 Å2
Refinement stepCycle: 1 / Resolution: 3.14→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 461 17 5982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026073
X-RAY DIFFRACTIONr_bond_other_d0.010.0215810
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9918204
X-RAY DIFFRACTIONr_angle_other_deg1.6653.02513273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62122.656256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11615900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5031540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026620
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021484
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3412.7122812
X-RAY DIFFRACTIONr_mcbond_other1.3412.7112811
X-RAY DIFFRACTIONr_mcangle_it2.1984.0683508
X-RAY DIFFRACTIONr_mcangle_other2.1974.0693509
X-RAY DIFFRACTIONr_scbond_it1.9773.1233261
X-RAY DIFFRACTIONr_scbond_other1.9773.1243262
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1154.5664697
X-RAY DIFFRACTIONr_long_range_B_refined5.14822.2966551
X-RAY DIFFRACTIONr_long_range_B_other5.14822.3026552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A103990.05
12B103990.05
21A103340.06
22C103340.06
31A103650.05
32D103650.05
41B103800.06
42C103800.06
51B103980.05
52D103980.05
61C104670.05
62D104670.05
LS refinement shellResolution: 3.145→3.227 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 101 -
Rwork0.272 1846 -
obs--82.36 %
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)
11.7272-0.2526-0.3522.9295-1.37173.38120.01160.2865-0.2016-0.17810.0211-0.08530.2747-0.033-0.03270.0251-0.0077-0.00180.3265-0.09460.0459-163.849129.3587-2.7113
22.42190.9084-0.54693.8675-1.49352.3211-0.01720.2504-0.17290.01720.0663-0.16780.23270.1323-0.04910.03390.0395-0.02040.3402-0.09350.0381-136.746229.3034-1.8753
33.03111.53340.47153.1788-0.4111.73740.07110.0115-0.23020.2044-0.0314-0.10390.22320.2465-0.03970.05960.0594-0.00890.3225-0.05950.0295-118.101228.920917.7029
42.2281.67490.59453.4210.53412.3620.0027-0.0842-0.24710.18880.02730.0150.21530.254-0.030.0360.04380.02050.30740.04250.0481-118.928828.867944.6558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 179
2X-RAY DIFFRACTION1A201 - 205
3X-RAY DIFFRACTION2B4 - 179
4X-RAY DIFFRACTION2B201 - 207
5X-RAY DIFFRACTION3C4 - 179
6X-RAY DIFFRACTION3C201 - 208
7X-RAY DIFFRACTION4D4 - 179
8X-RAY DIFFRACTION4D201 - 207

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