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- PDB-3w9t: pore-forming CEL-III -

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Basic information

Entry
Database: PDB / ID: 3w9t
Titlepore-forming CEL-III
ComponentsHemolytic lectin CEL-III
KeywordsTOXIN / Hemolytic lectin / Pore forming toxin
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / hemolysis in another organism / lactose binding / galactose binding ...positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / hemolysis in another organism / lactose binding / galactose binding / protein O-linked glycosylation / protein homooligomerization / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / magnesium ion binding / Golgi apparatus / extracellular space
Similarity search - Function
hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
lactulose / Galactose/N-acetylgalactosamine-binding lectin CEL-III
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.9 Å
AuthorsUnno, H. / Goda, S. / Hatakeyama, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Hemolytic lectin CEL-III heptamer reveals its transmembrane pore-formation mechanism
Authors: Unno, H. / Goda, S. / Hatakeyama, T.
History
DepositionApr 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Other
Revision 2.0Jul 25, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_nat / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 3.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolytic lectin CEL-III
C: Hemolytic lectin CEL-III
G: Hemolytic lectin CEL-III
B: Hemolytic lectin CEL-III
F: Hemolytic lectin CEL-III
E: Hemolytic lectin CEL-III
D: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,934102
Polymers332,1657
Non-polymers14,76995
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36080 Å2
ΔGint-101 kcal/mol
Surface area124050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.800, 228.650, 133.020
Angle α, β, γ (deg.)90.00, 127.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.715623, -0.681754, 0.15197), (0.682308, 0.635745, -0.360949), (0.149465, 0.361994, 0.92012)71.19553, -54.07935, -40.51479
3given(0.678702, 0.722479, 0.131865), (-0.720887, 0.621072, 0.307557), (0.140306, -0.303799, 0.942348)-8.93051, 101.91695, 3.64025
4given(0.006637, 0.874369, 0.485217), (-0.889714, -0.216333, 0.402006), (0.45647, -0.434372, 0.776502)55.22257, 172.51936, -25.34215
5given(-0.562523, 0.386421, 0.730922), (-0.408928, -0.898388, 0.160243), (0.718572, -0.208754, 0.663382)148.05255, 160.72713, -66.96054
6given(-0.543318, -0.395233, 0.740673), (0.382098, -0.901991, -0.201028), (0.747534, 0.173787, 0.641086)192.59212, 74.26899, -94.74038
7given(-0.010275, -0.875096, 0.483841), (0.874593, -0.242431, -0.419897), (0.484748, 0.418849, 0.767844)165.11728, -19.32623, -79.9135

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Components

#1: Protein
Hemolytic lectin CEL-III


Mass: 47452.164 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q868M7*PLUS
#2: Polysaccharide...
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 37
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 30% PEG400, 0.1M CdCl2, 0.1M sodium acetate, 10mM CaCl2, 0.1M lactulose, pH 4.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2010
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→53.5 Å / Num. obs: 113863 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIR / Resolution: 2.9→48.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / SU B: 37.412 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 1.039 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27305 5691 5 %RANDOM
Rwork0.23942 ---
obs0.24108 107985 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20.1 Å2
2--0.39 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23191 0 909 75 24175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9833546
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.65153017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53625.4821162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.109153836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.85415126
X-RAY DIFFRACTIONr_chiral_restr0.1340.23812
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118368
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 420 -
Rwork0.339 7991 -
obs--99.14 %
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)
10.3767-0.4276-0.12850.75940.15710.3207-0.1173-0.03770.09450.16320.1254-0.00320.0948-0.0952-0.00810.15890.09190.03530.27350.00440.106783.3228105.9592-14.6935
20.33270.0288-0.20820.2799-0.08830.3092-0.05920.0121-0.1527-0.0268-0.00520.0620.1365-0.16240.06430.2179-0.12170.090.28010.03930.149263.503933.6309-5.4994
30.80530.14720.05870.72230.37120.3595-0.12530.00380.3946-0.21510.0610.1487-0.11910.01750.06430.28260.0023-0.03260.13930.02710.215121.2997103.2956-32.6771
40.3954-0.25850.02440.38580.0530.1665-0.1538-0.0434-0.17260.04150.08680.20420.08-0.00590.0670.1856-0.00980.1060.26140.09420.165657.456775.2413-2.7634
50.94540.3261-0.11340.59440.24110.2088-0.25680.05220.0782-0.21650.22130.0646-0.00590.03950.03550.4533-0.03450.08210.37520.03270.0524142.700568.4932-42.0606
60.8101-0.0995-0.10350.35020.02420.0884-0.03270.0975-0.1468-0.0622-0.02650.02190.09670.07860.05920.33460.08810.0990.3376-0.0050.06131.847328.1256-37.226
70.23490.1665-0.08210.504-0.02540.2574-0.01860.0083-0.0877-0.0639-0.0633-0.09560.23470.03060.08190.30050.00160.07880.09990.00040.051296.508912.8579-21.073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 432
2X-RAY DIFFRACTION1A1001 - 1013
3X-RAY DIFFRACTION2C1 - 432
4X-RAY DIFFRACTION2C1001 - 1013
5X-RAY DIFFRACTION3G1 - 432
6X-RAY DIFFRACTION3G501 - 513
7X-RAY DIFFRACTION4B1 - 432
8X-RAY DIFFRACTION4B501 - 514
9X-RAY DIFFRACTION5F1 - 432
10X-RAY DIFFRACTION5F501 - 513
11X-RAY DIFFRACTION6E1 - 432
12X-RAY DIFFRACTION6E501 - 514
13X-RAY DIFFRACTION7D1 - 432
14X-RAY DIFFRACTION7D501 - 513

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